From 226bfda5a920147df495f3bbdbaf43781694fb7b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 13:23:12 +1300 Subject: [PATCH 01/49] Multiple changes --- .github/include.yaml | 10 +++ .github/workflows/ci.yml | 115 ++++++++++++++++------------ .gitignore | 2 + cleanNXF.sh | 4 + conf/test.config | 13 ++-- main.nf | 21 +++-- modules/local/utils/main.nf | 44 +++++++++++ nextflow.config | 78 +++++++------------ nf-test.config | 10 +++ test/nf-test/nextflow.config | 22 ++++++ test/nf-test/tiny/main.nf.test | 32 ++++++++ test/nf-test/tiny/main.nf.test.snap | 42 ++++++++++ 12 files changed, 284 insertions(+), 109 deletions(-) create mode 100644 .github/include.yaml create mode 100644 modules/local/utils/main.nf create mode 100644 nf-test.config create mode 100644 test/nf-test/nextflow.config create mode 100644 test/nf-test/tiny/main.nf.test create mode 100644 test/nf-test/tiny/main.nf.test.snap diff --git a/.github/include.yaml b/.github/include.yaml new file mode 100644 index 0000000..5d850e1 --- /dev/null +++ b/.github/include.yaml @@ -0,0 +1,10 @@ +".": + - ./.github/workflows/** + - ./nf-test.config +tests: + - ./assets/* + - ./bin/* + - ./conf/* + - ./main.nf + - ./nextflow_schema.json + - ./nextflow.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c27abd..43d4c6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,78 +1,99 @@ name: EDTA Nextflow CI on: - push: - branches: - - nextflow_reboot pull_request: - branches: - - nextflow_reboot env: NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + NFT_WORKDIR: "~" + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true - jobs: + nf-test-changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + nf_test_files: ${{ steps.list.outputs.components }} + steps: + - uses: actions/checkout@v4.2.1 + with: + fetch-depth: 0 + + - name: List nf-test files + id: list + uses: adamrtalbot/detect-nf-test-changes@v0.0.4 + with: + head: ${{ github.sha }} + base: origin/${{ github.base_ref }} + include: .github/include.yaml + + - name: print list of nf-test files + run: | + echo ${{ steps.list.outputs.components }} + test: - name: Run pipeline with test data - # Only run on push if this is the jguhlin nextflow_reboot branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'jguhlin/EDTA') }}" + name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} + needs: [nf-test-changes] + if: needs.nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - nextflow: - - '24.04.4' + NXF_VER: + - "24.04.2" + + nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - docker - - singularity - - conda + - "docker" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@v4.2.1 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 with: - version: ${{ matrix.nextflow }} + version: "${{ matrix.NXF_VER }}" - # - name: Disk space cleanup - # uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - # Will be needed with large data sets. Can take long to run + - uses: actions/setup-python@v5.2.0 + with: + python-version: "3.11" + architecture: "x64" - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' + - name: Install pdiff to see diff between nf-test snapshots run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + python -m pip install --upgrade pip + pip install pdiff + + - uses: nf-core/setup-nf-test@v1.1.2 with: - miniconda-version: "latest" - auto-update-conda: true - channels: conda-forge,bioconda + version: 0.9.0 - - name: Conda setup - if: matrix.profile == 'conda' + - name: Disk space cleanup + if: matrix.nf_test_files == 'tests/stub/main.nf.test' + uses: jlumbroso/free-disk-space@v1.3.1 + + - name: Run nf-test run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH + nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" + + confirm-pass: + runs-on: ubuntu-latest + needs: [test] + if: always() + steps: + - name: All tests ok + if: ${{ !contains(needs.*.result, 'failure') }} + run: exit 0 + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 - - name: Run pipeline with test data + - name: debug-print + if: always() run: | - nextflow run \ - ${GITHUB_WORKSPACE} \ - -profile ${{ matrix.profile }},test + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/.gitignore b/.gitignore index 9b1e821..f636970 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,5 @@ bin/TIR-Learner*/Module3/Maize_model.sav work/ .nextflow.log* .nextflow/* +results/ +.nf-test* diff --git a/cleanNXF.sh b/cleanNXF.sh index 8c64a3e..81b8d85 100755 --- a/cleanNXF.sh +++ b/cleanNXF.sh @@ -9,3 +9,7 @@ do rm -rf "work/$i" done echo "Cleaned work..." + +rm -f .nf-test.log +rm -rf .nf-test +echo "Cleaned nf-test..." diff --git a/conf/test.config b/conf/test.config index 1988af8..e921133 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,8 +1,11 @@ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { genomes = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' - // TODO: Replace with a larger genome as LTRHARVEST does not detect any LTRs on this one - - max_cpus = 2 - max_memory = '6.GB' - max_time = '1.hour' } \ No newline at end of file diff --git a/main.nf b/main.nf index b855de3..d49f489 100755 --- a/main.nf +++ b/main.nf @@ -16,11 +16,6 @@ params.exclude = '' params.maxint = 5000 params.outdir = 'results' -// Max resource options -params.max_cpus = 12 -params.max_memory = '16.GB' -params.max_time = '1.hour' - // TODO: Check inputed repeat libraries, CDS, etc... // TODO: Check exclude file @@ -30,11 +25,12 @@ include { LTRFINDER } from './modules/nf-core/ltrfinder/main include { CAT_CAT } from './modules/nf-core/cat/cat/main.nf' include { LTRRETRIEVER_LTRRETRIEVER } from './modules/nf-core/ltrretriever/ltrretriever/main.nf' include { TIRLEARNER } from './modules/gallvp/tirlearner/main.nf' -// nf-core -v modules -g https://github.com/GallVp/nxf-components.git install include { ANNOSINE } from './modules/gallvp/annosine/main.nf' include { REPEATMODELER_BUILDDATABASE } from './modules/nf-core/repeatmodeler/builddatabase/main.nf' include { REPEATMODELER_REPEATMODELER } from './modules/nf-core/repeatmodeler/repeatmodeler/main.nf' +include { softwareVersionsToYAML } from './modules/local/utils/main.nf' + // Test run: // ./main.nf -profile docker,test // ./main.nf -profile conda,test @@ -48,7 +44,7 @@ workflow { // Create a meta object for each genome ch_meta_genome = ch_genome.map { genome -> - meta = [:] + def meta = [:] meta.id = genome.baseName [ meta, genome ] @@ -152,4 +148,15 @@ workflow { ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + + // Function: Save versions + ch_versions_yml = softwareVersionsToYAML(ch_versions) + | collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'software_versions.yml', + sort: true, + newLine: true, + cache: false + ) + } diff --git a/modules/local/utils/main.nf b/modules/local/utils/main.nf new file mode 100644 index 0000000..fee91f3 --- /dev/null +++ b/modules/local/utils/main.nf @@ -0,0 +1,44 @@ +// +// Generate workflow version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index d0b0bfa..12a89b6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,38 +1,38 @@ process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' @@ -43,6 +43,15 @@ process { } } +// Max resources +process { + resourceLimits = [ + cpus: 12, + memory: '16.GB', + time: '1.hour' + ] +} + profiles { singularity { singularity.enabled = true @@ -82,40 +91,9 @@ conda { } manifest { + name = 'jguhlin/EDTA' nextflowVersion = '!>=23.04.0' + version = '0.1.0dev' } includeConfig 'conf/modules.config' - -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } - } -} \ No newline at end of file diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..c3a9a1e --- /dev/null +++ b/nf-test.config @@ -0,0 +1,10 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "test/nf-test/nextflow.config" + + plugins { + load "nft-bam@0.4.0" + load "nft-utils@0.0.3" + } +} diff --git a/test/nf-test/nextflow.config b/test/nf-test/nextflow.config new file mode 100644 index 0000000..ed1a805 --- /dev/null +++ b/test/nf-test/nextflow.config @@ -0,0 +1,22 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +} + +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} diff --git a/test/nf-test/tiny/main.nf.test b/test/nf-test/tiny/main.nf.test new file mode 100644 index 0000000..5022c49 --- /dev/null +++ b/test/nf-test/tiny/main.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test with a tiny genome" + script "main.nf" + + test("tiny genome") { + + when { + params { + genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + outdir = "$outputDir" + } + } + + then { + def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + assertAll( + { assert workflow.success}, + { assert snapshot( + [ + 'successful tasks': workflow.trace.succeeded().size(), + 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), + 'stable paths': stable_path + ] + ).match() } + ) + } + + } + +} diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap new file mode 100644 index 0000000..a61631f --- /dev/null +++ b/test/nf-test/tiny/main.nf.test.snap @@ -0,0 +1,42 @@ +{ + "tiny genome": { + "content": [ + { + "successful tasks": 7, + "versions": { + "ANNOSINE": { + "annosine": "2.0.7" + }, + "CAT_CAT": { + "pigz": "2.3.4" + }, + "LTRFINDER": { + "LTR_FINDER_parallel": "v1.1", + "ltr_finder": "v1.07" + }, + "LTRHARVEST": { + "LTR_HARVEST_parallel": "v1.1", + "genometools": "1.6.5" + }, + "LTRRETRIEVER_LTRRETRIEVER": { + "LTR_retriever": "v2.9.9" + }, + "TIRLEARNER": { + "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + }, + "Workflow": { + "jguhlin/EDTA": "v0.1.0dev" + } + }, + "stable paths": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-25T13:20:57.770583" + } +} \ No newline at end of file From 69c12641abdb87c3fea4a3f369664091af04e203 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 14:44:00 +1300 Subject: [PATCH 02/49] Updated test CI --- main.nf | 6 ++++ test/nf-test/small/main.nf.test | 32 +++++++++++++++++++ test/nf-test/small/main.nf.test.snap | 48 ++++++++++++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 test/nf-test/small/main.nf.test create mode 100644 test/nf-test/small/main.nf.test.snap diff --git a/main.nf b/main.nf index d49f489..091684c 100755 --- a/main.nf +++ b/main.nf @@ -150,6 +150,12 @@ workflow { // Function: Save versions + ch_versions = ch_versions + | unique + | map { yml -> + if ( yml ) { yml } + } + ch_versions_yml = softwareVersionsToYAML(ch_versions) | collectFile( storeDir: "${params.outdir}/pipeline_info", diff --git a/test/nf-test/small/main.nf.test b/test/nf-test/small/main.nf.test new file mode 100644 index 0000000..4cb9c26 --- /dev/null +++ b/test/nf-test/small/main.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test with a small genome" + script "main.nf" + + test("small genome") { + + when { + params { + genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" + outdir = "$outputDir" + } + } + + then { + def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + assertAll( + { assert workflow.success}, + { assert snapshot( + [ + 'successful tasks': workflow.trace.succeeded().size(), + 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), + 'stable paths': stable_path + ] + ).match() } + ) + } + + } + +} diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap new file mode 100644 index 0000000..d53e834 --- /dev/null +++ b/test/nf-test/small/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "small genome": { + "content": [ + { + "successful tasks": 9, + "versions": { + "ANNOSINE": { + "annosine": "2.0.7" + }, + "CAT_CAT": { + "pigz": "2.3.4" + }, + "LTRFINDER": { + "LTR_FINDER_parallel": "v1.1", + "ltr_finder": "v1.07" + }, + "LTRHARVEST": { + "LTR_HARVEST_parallel": "v1.1", + "genometools": "1.6.5" + }, + "LTRRETRIEVER_LTRRETRIEVER": { + "LTR_retriever": "v2.9.9" + }, + "REPEATMODELER_BUILDDATABASE": { + "repeatmodeler": "2.0.5" + }, + "REPEATMODELER_REPEATMODELER": { + "repeatmodeler": "2.0.5" + }, + "TIRLEARNER": { + "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + }, + "Workflow": { + "jguhlin/EDTA": "v0.1.0dev" + } + }, + "stable paths": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-25T13:53:22.07666" + } +} \ No newline at end of file From 2bfe387e32dae9378f976b752c9613a0c2bbb2b4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 15:23:50 +1300 Subject: [PATCH 03/49] Added missing modules, profiles and manifest fields --- .github/workflows/ci.yml | 18 ++- conf/modules.config | 10 +- main.nf | 147 +----------------- modules.json | 10 ++ modules/gallvp/gunzip/environment.yml | 7 + modules/gallvp/gunzip/main.nf | 55 +++++++ modules/gallvp/gunzip/meta.yml | 47 ++++++ modules/gallvp/gunzip/tests/main.nf.test | 121 ++++++++++++++ modules/gallvp/gunzip/tests/main.nf.test.snap | 134 ++++++++++++++++ modules/gallvp/gunzip/tests/nextflow.config | 5 + modules/gallvp/gunzip/tests/tags.yml | 2 + modules/nf-core/gunzip/environment.yml | 7 + modules/nf-core/gunzip/main.nf | 55 +++++++ modules/nf-core/gunzip/meta.yml | 47 ++++++ modules/nf-core/gunzip/tests/main.nf.test | 121 ++++++++++++++ .../nf-core/gunzip/tests/main.nf.test.snap | 134 ++++++++++++++++ modules/nf-core/gunzip/tests/nextflow.config | 5 + modules/nf-core/gunzip/tests/tags.yml | 2 + nextflow.config | 4 +- workflows/edta.nf | 144 +++++++++++++++++ 20 files changed, 920 insertions(+), 155 deletions(-) create mode 100644 modules/gallvp/gunzip/environment.yml create mode 100644 modules/gallvp/gunzip/main.nf create mode 100644 modules/gallvp/gunzip/meta.yml create mode 100644 modules/gallvp/gunzip/tests/main.nf.test create mode 100644 modules/gallvp/gunzip/tests/main.nf.test.snap create mode 100644 modules/gallvp/gunzip/tests/nextflow.config create mode 100644 modules/gallvp/gunzip/tests/tags.yml create mode 100644 modules/nf-core/gunzip/environment.yml create mode 100644 modules/nf-core/gunzip/main.nf create mode 100644 modules/nf-core/gunzip/meta.yml create mode 100644 modules/nf-core/gunzip/tests/main.nf.test create mode 100644 modules/nf-core/gunzip/tests/main.nf.test.snap create mode 100644 modules/nf-core/gunzip/tests/nextflow.config create mode 100644 modules/nf-core/gunzip/tests/tags.yml create mode 100644 workflows/edta.nf diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 43d4c6c..20d4b62 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,10 +7,13 @@ env: NFT_WORKDIR: "~" NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true + jobs: nf-test-changes: name: Check for changes @@ -46,8 +49,7 @@ jobs: - "24.04.2" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] - profile: - - "docker" + profile: [conda, docker, singularity] steps: - name: Check out pipeline code @@ -71,10 +73,16 @@ jobs: - uses: nf-core/setup-nf-test@v1.1.2 with: version: 0.9.0 + + - name: Setup apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Disk space cleanup - if: matrix.nf_test_files == 'tests/stub/main.nf.test' - uses: jlumbroso/free-disk-space@v1.3.1 + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR - name: Run nf-test run: | diff --git a/conf/modules.config b/conf/modules.config index c274e02..81d11dc 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,22 +1,22 @@ process { - withName: 'LTRHARVEST' { + withName: 'EDTA:LTRHARVEST' { ext.args = '-size 1000000 -time 300' ext.prefix = { "${meta.id}_ltrharvest" } } - withName: 'LTRFINDER' { + withName: 'EDTA:LTRFINDER' { ext.args = '-harvest_out -size 1000000 -time 300' } - withName: 'CAT_CAT' { + withName: 'EDTA:CAT_CAT' { ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } } - withName: 'ANNOSINE' { + withName: 'EDTA:ANNOSINE' { ext.args = '--num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' } - withName: 'REPEATMODELER_REPEATMODELER' { + withName: 'EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' } diff --git a/main.nf b/main.nf index 091684c..fa74a8b 100755 --- a/main.nf +++ b/main.nf @@ -16,153 +16,12 @@ params.exclude = '' params.maxint = 5000 params.outdir = 'results' -// TODO: Check inputed repeat libraries, CDS, etc... -// TODO: Check exclude file - -include { SANITIZE_HEADERS } from './modules/local/sanitize/main.nf' -include { LTRHARVEST } from './modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from './modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from './modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from './modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { TIRLEARNER } from './modules/gallvp/tirlearner/main.nf' -include { ANNOSINE } from './modules/gallvp/annosine/main.nf' -include { REPEATMODELER_BUILDDATABASE } from './modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from './modules/nf-core/repeatmodeler/repeatmodeler/main.nf' - -include { softwareVersionsToYAML } from './modules/local/utils/main.nf' +include { EDTA } from './workflows/edta.nf' // Test run: // ./main.nf -profile docker,test // ./main.nf -profile conda,test -workflow { - - // Versions channel - ch_versions = Channel.empty() - - - ch_genome = Channel.fromPath(params.genomes) - - // Create a meta object for each genome - ch_meta_genome = ch_genome.map { genome -> - def meta = [:] - meta.id = genome.baseName - - [ meta, genome ] - } - - // MODULE: SANITIZE_HEADERS - SANITIZE_HEADERS ( ch_meta_genome ) - - ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta - - // MODULE: LTRHARVEST - LTRHARVEST ( ch_sanitized_fasta ) - - ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 - ch_ltrharvest_scn = LTRHARVEST.out.scn - - ch_versions = ch_versions.mix(LTRHARVEST.out.versions) - - // MODULE: LTRFINDER - LTRFINDER { ch_sanitized_fasta } - - ch_ltrfinder_gff3 = LTRFINDER.out.gff - ch_ltrfinder_scn = LTRFINDER.out.scn - - ch_versions = ch_versions.mix(LTRFINDER.out.versions) - - // MODULE: CAT_CAT - ch_cat_cat_inputs = ch_ltrharvest_scn - | join(ch_ltrfinder_scn) - | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } - CAT_CAT ( ch_cat_cat_inputs ) - - ch_ltr_candidates = CAT_CAT.out.file_out - ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) - - // MODULE: LTRRETRIEVER_LTRRETRIEVER - ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) - - LTRRETRIEVER_LTRRETRIEVER ( - ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, - ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, - [], - [], - [] - ) - - ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log - ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list - ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out - ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff - ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib - ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) - - // MODULE: TIRLEARNER - TIRLEARNER ( - ch_sanitized_fasta, - params.species - ) - - ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff - ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) - - // These can also run in parallel - // MODULE: ANNOSINE - ANNOSINE ( - ch_sanitized_fasta, - 3 // mode - ) - - // Currently it's a topic, so need to fix that - ch_versions = ch_versions.mix(ANNOSINE.out.versions) - cb_annosine_seed_sine = ANNOSINE.out.fa - - // MODULE: REPEATMODELER_BUILDDATABASE - ch_repeatmodeler_inputs = ch_sanitized_fasta - | map { meta, fasta -> - def size = fasta.size() - def size_threshold = 100_000 // bytes -> bp - - // TODO: Not the best way to set a size threshould - // but it is simple - // This is needed to avoid, - // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. - if ( size < size_threshold ) { - log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" - return null - } - - return [ meta, fasta ] - } - | filter { it } - - REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) - - ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db - ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) - - // MODULE: REPEATMODELER_REPEATMODELER - REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) - - ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta - ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) - - - // Function: Save versions - ch_versions = ch_versions - | unique - | map { yml -> - if ( yml ) { yml } - } - - ch_versions_yml = softwareVersionsToYAML(ch_versions) - | collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'software_versions.yml', - sort: true, - newLine: true, - cache: false - ) +workflow { + EDTA() } diff --git a/modules.json b/modules.json index 746eb3b..f9eedd5 100644 --- a/modules.json +++ b/modules.json @@ -10,6 +10,11 @@ "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] }, + "gunzip": { + "branch": "main", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", + "installed_by": ["modules"] + }, "tirlearner": { "branch": "main", "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", @@ -26,6 +31,11 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "gunzip": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, "ltrfinder": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", diff --git a/modules/gallvp/gunzip/environment.yml b/modules/gallvp/gunzip/environment.yml new file mode 100644 index 0000000..c779485 --- /dev/null +++ b/modules/gallvp/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/gallvp/gunzip/main.nf b/modules/gallvp/gunzip/main.nf new file mode 100644 index 0000000..5e67e3b --- /dev/null +++ b/modules/gallvp/gunzip/main.nf @@ -0,0 +1,55 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ + $args \\ + $archive \\ + > $gunzip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/gallvp/gunzip/meta.yml b/modules/gallvp/gunzip/meta.yml new file mode 100644 index 0000000..9066c03 --- /dev/null +++ b/modules/gallvp/gunzip/meta.yml @@ -0,0 +1,47 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/gallvp/gunzip/tests/main.nf.test b/modules/gallvp/gunzip/tests/main.nf.test new file mode 100644 index 0000000..f661057 --- /dev/null +++ b/modules/gallvp/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_gallvp" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/gunzip/tests/main.nf.test.snap b/modules/gallvp/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..069967e --- /dev/null +++ b/modules/gallvp/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/gallvp/gunzip/tests/nextflow.config b/modules/gallvp/gunzip/tests/nextflow.config new file mode 100644 index 0000000..dec7764 --- /dev/null +++ b/modules/gallvp/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/gallvp/gunzip/tests/tags.yml b/modules/gallvp/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/gallvp/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 0000000..c779485 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf new file mode 100644 index 0000000..5e67e3b --- /dev/null +++ b/modules/nf-core/gunzip/main.nf @@ -0,0 +1,55 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ + $args \\ + $archive \\ + > $gunzip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml new file mode 100644 index 0000000..9066c03 --- /dev/null +++ b/modules/nf-core/gunzip/meta.yml @@ -0,0 +1,47 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 0000000..776211a --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..069967e --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 0000000..dec7764 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/nextflow.config b/nextflow.config index 12a89b6..34dfae1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -92,8 +92,10 @@ conda { manifest { name = 'jguhlin/EDTA' - nextflowVersion = '!>=23.04.0' + description = 'Extensive de-novo TE Annotator on Nextflow' + manifest.author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' version = '0.1.0dev' + nextflowVersion = '!>=23.04.0' } includeConfig 'conf/modules.config' diff --git a/workflows/edta.nf b/workflows/edta.nf new file mode 100644 index 0000000..df8b2d9 --- /dev/null +++ b/workflows/edta.nf @@ -0,0 +1,144 @@ +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' +include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' + +include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' + +workflow EDTA { + + // Versions channel + ch_versions = Channel.empty() + + + ch_genome = Channel.fromPath(params.genomes) + + // Create a meta object for each genome + ch_meta_genome = ch_genome.map { genome -> + def meta = [:] + meta.id = genome.baseName + + [ meta, genome ] + } + + // MODULE: SANITIZE_HEADERS + SANITIZE_HEADERS ( ch_meta_genome ) + + ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta + + // MODULE: LTRHARVEST + LTRHARVEST ( ch_sanitized_fasta ) + + ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 + ch_ltrharvest_scn = LTRHARVEST.out.scn + + ch_versions = ch_versions.mix(LTRHARVEST.out.versions) + + // MODULE: LTRFINDER + LTRFINDER { ch_sanitized_fasta } + + ch_ltrfinder_gff3 = LTRFINDER.out.gff + ch_ltrfinder_scn = LTRFINDER.out.scn + + ch_versions = ch_versions.mix(LTRFINDER.out.versions) + + // MODULE: CAT_CAT + ch_cat_cat_inputs = ch_ltrharvest_scn + | join(ch_ltrfinder_scn) + | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } + CAT_CAT ( ch_cat_cat_inputs ) + + ch_ltr_candidates = CAT_CAT.out.file_out + ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) + + // MODULE: LTRRETRIEVER_LTRRETRIEVER + ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) + + LTRRETRIEVER_LTRRETRIEVER ( + ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, + ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, + [], + [], + [] + ) + + ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log + ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list + ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out + ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff + ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib + ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) + + // MODULE: TIRLEARNER + TIRLEARNER ( + ch_sanitized_fasta, + params.species + ) + + ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff + ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + + // These can also run in parallel + // MODULE: ANNOSINE + ANNOSINE ( + ch_sanitized_fasta, + 3 // mode + ) + + // Currently it's a topic, so need to fix that + ch_versions = ch_versions.mix(ANNOSINE.out.versions) + cb_annosine_seed_sine = ANNOSINE.out.fa + + // MODULE: REPEATMODELER_BUILDDATABASE + ch_repeatmodeler_inputs = ch_sanitized_fasta + | map { meta, fasta -> + def size = fasta.size() + def size_threshold = 100_000 // bytes -> bp + + // TODO: Not the best way to set a size threshould + // but it is simple + // This is needed to avoid, + // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. + if ( size < size_threshold ) { + log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" + return null + } + + return [ meta, fasta ] + } + | filter { it } + + REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) + + ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db + ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) + + // MODULE: REPEATMODELER_REPEATMODELER + REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) + + ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta + ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + + + // Function: Save versions + ch_versions = ch_versions + | unique + | map { yml -> + if ( yml ) { yml } + } + + ch_versions_yml = softwareVersionsToYAML(ch_versions) + | collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'software_versions.yml', + sort: true, + newLine: true, + cache: false + ) + +} \ No newline at end of file From 3c9b2f81744b3479ab8ff506811c803fbefa3e5e Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 15:41:03 +1300 Subject: [PATCH 04/49] Now using EDTA's test genome for the small test --- test/nf-test/small/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/nf-test/small/main.nf.test b/test/nf-test/small/main.nf.test index 4cb9c26..7d40a02 100644 --- a/test/nf-test/small/main.nf.test +++ b/test/nf-test/small/main.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { when { params { - genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" + genomes = "https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa" outdir = "$outputDir" } } From 4b7bc1bf6ba3aaf62ba6223b369ae93acc387e5d Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 21:42:17 +1300 Subject: [PATCH 05/49] Updated PR template --- .github/PULL_REQUEST_TEMPLATE.md | 11 +++++------ nextflow.config | 2 +- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index a78bd61..7919df0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,19 +1,18 @@ ## PR checklist -- [ ] PR to `nextflow_reboot` branch -- [ ] `conda` and `container` directives. -- [ ] Docker container + singularity container (optional) +For Nextflow implementation, + +- [ ] `conda` and `container` directives are included for each process +- [ ] Docker container + singularity container (optional) are included for each process - [ ] Flow `meta.id` with each data channel - [ ] Use nf-core resource labels such as `process_high` - [ ] Used nf-core module diff --git a/nextflow.config b/nextflow.config index 34dfae1..ccf5850 100644 --- a/nextflow.config +++ b/nextflow.config @@ -93,7 +93,7 @@ conda { manifest { name = 'jguhlin/EDTA' description = 'Extensive de-novo TE Annotator on Nextflow' - manifest.author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' + author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' version = '0.1.0dev' nextflowVersion = '!>=23.04.0' } From 0195b02da466f55d3a6bf85abcf1fd03a9b204b1 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 22:21:39 +1300 Subject: [PATCH 06/49] Added fasta_helitronscanner_scan_draw --- conf/modules.config | 19 +++ modules.json | 19 +++ .../helitronscanner/draw/environment.yml | 7 + modules/gallvp/helitronscanner/draw/main.nf | 73 ++++++++ modules/gallvp/helitronscanner/draw/meta.yml | 69 ++++++++ .../helitronscanner/draw/tests/main.nf.test | 159 ++++++++++++++++++ .../draw/tests/main.nf.test.snap | 80 +++++++++ .../draw/tests/nextflow.config | 5 + .../helitronscanner/scan/environment.yml | 5 + modules/gallvp/helitronscanner/scan/main.nf | 72 ++++++++ modules/gallvp/helitronscanner/scan/meta.yml | 60 +++++++ .../helitronscanner/scan/tests/main.nf.test | 148 ++++++++++++++++ .../scan/tests/main.nf.test.snap | 104 ++++++++++++ .../fasta_helitronscanner_scan_draw/main.nf | 86 ++++++++++ .../fasta_helitronscanner_scan_draw/meta.yml | 45 +++++ .../tests/main.nf.test | 97 +++++++++++ .../tests/main.nf.test.snap | 137 +++++++++++++++ .../tests/nextflow.config | 20 +++ workflows/edta.nf | 26 +-- 19 files changed, 1220 insertions(+), 11 deletions(-) create mode 100644 modules/gallvp/helitronscanner/draw/environment.yml create mode 100644 modules/gallvp/helitronscanner/draw/main.nf create mode 100644 modules/gallvp/helitronscanner/draw/meta.yml create mode 100644 modules/gallvp/helitronscanner/draw/tests/main.nf.test create mode 100644 modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap create mode 100644 modules/gallvp/helitronscanner/draw/tests/nextflow.config create mode 100644 modules/gallvp/helitronscanner/scan/environment.yml create mode 100644 modules/gallvp/helitronscanner/scan/main.nf create mode 100644 modules/gallvp/helitronscanner/scan/meta.yml create mode 100644 modules/gallvp/helitronscanner/scan/tests/main.nf.test create mode 100644 modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config diff --git a/conf/modules.config b/conf/modules.config index 81d11dc..e70a6ea 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -19,5 +19,24 @@ process { withName: 'EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '-pure_helitron' + } } \ No newline at end of file diff --git a/modules.json b/modules.json index f9eedd5..5d34d4e 100644 --- a/modules.json +++ b/modules.json @@ -15,12 +15,31 @@ "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["modules"] }, + "helitronscanner/draw": { + "branch": "main", + "git_sha": "929d59d82f2e90fe79eb6f93d1ae739f22a894e1", + "installed_by": ["fasta_helitronscanner_scan_draw"] + }, + "helitronscanner/scan": { + "branch": "main", + "git_sha": "929d59d82f2e90fe79eb6f93d1ae739f22a894e1", + "installed_by": ["fasta_helitronscanner_scan_draw"] + }, "tirlearner": { "branch": "main", "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] } } + }, + "subworkflows": { + "gallvp": { + "fasta_helitronscanner_scan_draw": { + "branch": "main", + "git_sha": "970e3af38229845dd38c13d29b0905651a8e61f0", + "installed_by": ["subworkflows"] + } + } } }, "https://github.com/nf-core/modules.git": { diff --git a/modules/gallvp/helitronscanner/draw/environment.yml b/modules/gallvp/helitronscanner/draw/environment.yml new file mode 100644 index 0000000..479f61c --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::helitronscanner=1.0" diff --git a/modules/gallvp/helitronscanner/draw/main.nf b/modules/gallvp/helitronscanner/draw/main.nf new file mode 100644 index 0000000..16ee59a --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/main.nf @@ -0,0 +1,73 @@ +process HELITRONSCANNER_DRAW { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/helitronscanner:1.0--hdfd78af_0': + 'biocontainers/helitronscanner:1.0--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(head) + tuple val(meta3), path(tail) + + output: + tuple val(meta), path("*.draw") , emit: draw + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ( !task.memory ) { error '[HELITRONSCANNER_DRAW] Available memory not known. Specify process memory requirements to fix this.' } + def avail_mem = (task.memory.giga*0.8).intValue() + """ + # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) + # Check for container variable initialisation script and source it. + if [ -f "/usr/local/env-activate.sh" ]; then + set +u # Otherwise, errors out because of various unbound variables + . "/usr/local/env-activate.sh" + set -u + fi + + HelitronScanner \\ + pairends \\ + -Xmx${avail_mem}g \\ + -head_score $head \\ + -tail_score $tail \\ + -output ${prefix}.pairends \\ + ${args2} + + HelitronScanner \\ + draw \\ + -Xmx${avail_mem}g \\ + -pscore ${prefix}.pairends \\ + -g $fasta \\ + -output ${prefix}.draw \\ + ${args} + + mv ${prefix}.draw.hel.fa \\ + ${prefix}.draw + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.draw + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ +} diff --git a/modules/gallvp/helitronscanner/draw/meta.yml b/modules/gallvp/helitronscanner/draw/meta.yml new file mode 100644 index 0000000..96bd260 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/meta.yml @@ -0,0 +1,69 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "helitronscanner_draw" +description: HelitronScanner draw tool for Helitron transposons in genomes +keywords: + - genomics + - helitron + - scanner +tools: + - "helitronscanner": + description: "HelitronScanner uncovers a large overlooked cache of Helitron transposons + in many genomes" + homepage: "https://sourceforge.net/projects/helitronscanner" + documentation: "https://sourceforge.net/projects/helitronscanner" + tool_dev_url: "https://sourceforge.net/projects/helitronscanner" + doi: "10.1073/pnas.1410068111" + licence: ["GPL v3-or-later"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome data to scan for Helitrons + pattern: "*.{fa,fsa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - head: + type: file + description: Output of the HelitronScanner head command + pattern: "*.head" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tail: + type: file + description: Output of the HelitronScanner tail command + pattern: "*.tail" +output: + - draw: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.draw" + - "*.draw": + type: map + description: | + The draw output from HelitronScanner + pattern: "*.draw" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" + - "@jguhlin" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/helitronscanner/draw/tests/main.nf.test b/modules/gallvp/helitronscanner/draw/tests/main.nf.test new file mode 100644 index 0000000..331f563 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/main.nf.test @@ -0,0 +1,159 @@ +nextflow_process { + + name "Test Process HELITRONSCANNER_DRAW" + script "../main.nf" + config "./nextflow.config" + process "HELITRONSCANNER_DRAW" + + tag "modules" + tag "modules_gallvp" + tag "helitronscanner" + tag "helitronscanner/draw" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANHEAD') { + script "../../scan/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANTAIL') { + script "../../scan/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + } + + test("actinidia_chinensis-genome_1_fasta_gz-success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = HELITRONSCANNER_SCANHEAD.out.scan + input[2] = HELITRONSCANNER_SCANTAIL.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("sarscov2 - genome - success") { + + setup { + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANHEAD_SARSCOV2') { + script "../../scan/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANTAIL_SARSCOV2') { + script "../../scan/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = HELITRONSCANNER_SCANHEAD_SARSCOV2.out.scan + input[2] = HELITRONSCANNER_SCANTAIL_SARSCOV2.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.draw[0][1] != null }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = HELITRONSCANNER_SCANHEAD.out.scan + input[2] = HELITRONSCANNER_SCANTAIL.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap b/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap new file mode 100644 index 0000000..208d14d --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "actinidia_chinensis-genome_1_fasta_gz-success": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "1": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ], + "draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "versions": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:51:49.477212" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ], + "draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:52:47.744899" + }, + "sarscov2 - genome - success": { + "content": [ + [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:58:21.800568" + } +} \ No newline at end of file diff --git a/modules/gallvp/helitronscanner/draw/tests/nextflow.config b/modules/gallvp/helitronscanner/draw/tests/nextflow.config new file mode 100644 index 0000000..57f4900 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } +} diff --git a/modules/gallvp/helitronscanner/scan/environment.yml b/modules/gallvp/helitronscanner/scan/environment.yml new file mode 100644 index 0000000..ea89d39 --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::helitronscanner=1.0" diff --git a/modules/gallvp/helitronscanner/scan/main.nf b/modules/gallvp/helitronscanner/scan/main.nf new file mode 100644 index 0000000..0f748ab --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/main.nf @@ -0,0 +1,72 @@ +process HELITRONSCANNER_SCAN { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/helitronscanner:1.0--hdfd78af_0': + 'biocontainers/helitronscanner:1.0--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + val command + path lcv_filepath + val buffer_size + + output: + tuple val(meta), path("*.$command") , emit: scan + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + if ( command !in [ 'head', 'tail' ] ) error "[HELITRONSCANNER_SCAN] command argument should be 'head' or 'tail'" + if ( !task.memory ) { error '[HELITRONSCANNER_SCAN] Available memory not known. Specify process memory requirements to fix this.' } + + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def is_head = { command == 'head' }() + def subcommand = is_head ? 'scanHead' : 'scanTail' + def lcvs_file = is_head ? 'head.lcvs' : 'tail.lcvs' + def lcv_arg = lcv_filepath ? "-lcv_filepath $lcv_filepath" : "-lcv_filepath \$HELITRONSCANNER_TRAININGSET_PATH/$lcvs_file" + def avail_mem = (task.memory.giga*0.8).intValue() + """ + # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) + # Check for container variable initialisation script and source it. + if [ -f "/usr/local/env-activate.sh" ]; then + set +u # Otherwise, errors out because of various unbound variables + . "/usr/local/env-activate.sh" + set -u + fi + + HelitronScanner \\ + $subcommand \\ + -Xmx${avail_mem}g \\ + $lcv_arg \\ + -genome $fasta \\ + -buffer_size $buffer_size \\ + -threads_LCV $task.cpus \\ + $args \\ + -output ${prefix}.${command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ + + stub: + if ( command !in [ 'head', 'tail' ] ) error "[HELITRONSCANNER_SCAN] command argument should be 'head' or 'tail'" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.${command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ +} diff --git a/modules/gallvp/helitronscanner/scan/meta.yml b/modules/gallvp/helitronscanner/scan/meta.yml new file mode 100644 index 0000000..ed8f956 --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/meta.yml @@ -0,0 +1,60 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "helitronscanner_scan" +description: HelitronScanner scanHead and scanTail tools for Helitron transposons + in genomes +keywords: + - genomics + - helitron + - scanner +tools: + - "helitronscanner": + description: "HelitronScanner uncovers a large overlooked cache of Helitron transposons + in many genomes" + homepage: "https://sourceforge.net/projects/helitronscanner" + documentation: "https://sourceforge.net/projects/helitronscanner" + tool_dev_url: "https://sourceforge.net/projects/helitronscanner" + doi: "10.1073/pnas.1410068111" + licence: ["GPL v3-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome data to scan for Helitrons + pattern: "*.{fa,fsa,fasta}" + - - command: + type: string + description: Command to execute. One of [ 'head', 'tail' ] + - - lcv_filepath: + type: file + description: LCV file path. If not provided by setting it to [], the LCV file + packaged with the module will be used + pattern: "*.lcvs" + - - buffer_size: + type: integer + description: Genome slice size (use negative or zero for non-buffer, i.e. treat + every whole chromosome) +output: + - scan: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.$command": + type: file + description: Head or tail file depending on the command + pattern: "*.$command" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/helitronscanner/scan/tests/main.nf.test b/modules/gallvp/helitronscanner/scan/tests/main.nf.test new file mode 100644 index 0000000..55bcfed --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/tests/main.nf.test @@ -0,0 +1,148 @@ +nextflow_process { + + name "Test Process HELITRONSCANNER_SCAN" + script "../main.nf" + process "HELITRONSCANNER_SCAN" + + tag "modules" + tag "modules_gallvp" + tag "helitronscanner" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + } + + test("actinidia_chinensis - genome_1_fasta_gz - head - success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('2729827:1 2729980:1 2730005:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("actinidia_chinensis - genome_1_fasta_gz - tail - success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('7265:1 7951:1 9264:2 9398:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("sarscov2 - genome - head - success") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('113:2 236:1 1158:1 1754:2 1771:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stub - tail") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap b/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap new file mode 100644 index 0000000..ac7ae5e --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap @@ -0,0 +1,104 @@ +{ + "actinidia_chinensis - genome_1_fasta_gz - tail - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:51:54.403269" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.head:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ], + "scan": [ + [ + { + "id": "test" + }, + "test.head:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:52:10.250343" + }, + "sarscov2 - genome - head - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:43:05.068944" + }, + "stub - tail": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tail:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ], + "scan": [ + [ + { + "id": "test" + }, + "test.tail:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:39:42.225262" + }, + "actinidia_chinensis - genome_1_fasta_gz - head - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:51:18.942428" + } +} \ No newline at end of file diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf new file mode 100644 index 0000000..40c2541 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf @@ -0,0 +1,86 @@ +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_DRAW } from '../../../modules/gallvp/helitronscanner/draw/main.nf' + +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD_RC } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL_RC } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_DRAW as HELITRONSCANNER_DRAW_RC } from '../../../modules/gallvp/helitronscanner/draw/main.nf' + +workflow FASTA_HELITRONSCANNER_SCAN_DRAW { + + take: + ch_fasta // channel: [ val(meta), fasta ] + + main: + + ch_versions = Channel.empty() + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD + HELITRONSCANNER_SCAN_HEAD ( + ch_fasta, + 'head', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_head = HELITRONSCANNER_SCAN_HEAD.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_HEAD.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL + HELITRONSCANNER_SCAN_TAIL ( + ch_fasta, + 'tail', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_tail = HELITRONSCANNER_SCAN_TAIL.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_TAIL.out.versions) + + // MODULE: HELITRONSCANNER_DRAW + HELITRONSCANNER_DRAW ( + ch_fasta, + ch_helitronscanner_scan_head, + ch_helitronscanner_scan_tail + ) + + ch_helitronscanner_draw = HELITRONSCANNER_DRAW.out.draw + ch_versions = ch_versions.mix(HELITRONSCANNER_DRAW.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD_RC + HELITRONSCANNER_SCAN_HEAD_RC ( + ch_fasta, + 'head', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_head_rc = HELITRONSCANNER_SCAN_HEAD_RC.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_HEAD_RC.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL_RC + HELITRONSCANNER_SCAN_TAIL_RC ( + ch_fasta, + 'tail', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_tail_rc = HELITRONSCANNER_SCAN_TAIL_RC.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_TAIL_RC.out.versions) + + // MODULE: HELITRONSCANNER_DRAW as HELITRONSCANNER_DRAW_RC + HELITRONSCANNER_DRAW_RC ( + ch_fasta, + ch_helitronscanner_scan_head_rc, + ch_helitronscanner_scan_tail_rc + ) + + ch_helitronscanner_draw_rc = HELITRONSCANNER_DRAW_RC.out.draw + ch_versions = ch_versions.mix(HELITRONSCANNER_DRAW_RC.out.versions) + + emit: + helitronscanner_draw = ch_helitronscanner_draw // channel: [ val(meta), draw ] + helitronscanner_draw_rc = ch_helitronscanner_draw_rc // channel: [ val(meta), rc.draw ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml new file mode 100644 index 0000000..62c4b39 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml @@ -0,0 +1,45 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fasta_helitronscanner_scan_draw" +description: Find helitrons suing Helitronscanner scan, pairends and draw subcommands +keywords: + - helitron + - scan + - draw + - pairends + - repeat + - genomics + - fasta +components: + - helitronscanner/scan + - helitronscanner/draw +input: + - ch_fasta: + type: file + description: | + Genome fasta + Structure: [ val(meta), fasta ] + pattern: "*.fasta" +output: + - helitronscanner_draw: + type: file + description: | + Helitronscanner draw file + Structure: [ val(meta), draw ] + pattern: "*.draw" + - helitronscanner_draw_rc: + type: file + description: | + Helitronscanner reverse complement draw file + Structure: [ val(meta), rc.draw ] + pattern: "*.rc.draw" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" + - "@jguhlin" diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test new file mode 100644 index 0000000..7a9bd05 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test @@ -0,0 +1,97 @@ +nextflow_workflow { + + name "Test Subworkflow FASTA_HELITRONSCANNER_SCAN_DRAW" + script "../main.nf" + workflow "FASTA_HELITRONSCANNER_SCAN_DRAW" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_gallvp" + tag "subworkflows/fasta_helitronscanner_scan_draw" + + tag "helitronscanner/draw" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../../modules/gallvp/gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + } + + test("actinidia_chinensis - genome_1_fasta_gz") { + + when { + workflow { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } + + test("sarscov2 - genome") { + + when { + workflow { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.out.helitronscanner_draw }, // empty + { assert workflow.out.helitronscanner_draw_rc }, // empty + { assert snapshot( + workflow.out.versions + ).match() + } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } +} diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap new file mode 100644 index 0000000..f6b8077 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap @@ -0,0 +1,137 @@ +{ + "actinidia_chinensis - genome_1_fasta_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,7aeed0fdf50f8cb2516b2e92f456835e" + ] + ], + "2": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ], + "helitronscanner_draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "helitronscanner_draw_rc": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,7aeed0fdf50f8cb2516b2e92f456835e" + ] + ], + "versions": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T11:53:51.717511" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ], + "helitronscanner_draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "helitronscanner_draw_rc": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T11:54:17.824589" + }, + "sarscov2 - genome": { + "content": [ + [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T12:03:43.135817" + } +} \ No newline at end of file diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config new file mode 100644 index 0000000..b98d370 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + withName: 'HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } + + withName: 'HELITRONSCANNER_SCAN_HEAD_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'HELITRONSCANNER_SCAN_TAIL_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'HELITRONSCANNER_DRAW_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '-pure_helitron' + } +} diff --git a/workflows/edta.nf b/workflows/edta.nf index df8b2d9..357b427 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -1,14 +1,15 @@ -include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' -include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' -include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' -include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' - -include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' +include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' +include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' + +include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' workflow EDTA { @@ -124,6 +125,9 @@ workflow EDTA { ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW + FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) + // Function: Save versions ch_versions = ch_versions From 345341069f0e9767c6cab065855c6789b3f27104 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 22:39:10 +1300 Subject: [PATCH 07/49] Updated snapshots --- conf/modules.config | 8 ++++---- test/nf-test/small/main.nf.test.snap | 22 ++++++++++++++++++++-- test/nf-test/tiny/main.nf.test.snap | 22 ++++++++++++++++++++-- workflows/edta.nf | 4 ++++ 4 files changed, 48 insertions(+), 8 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e70a6ea..39b1af8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -20,21 +20,21 @@ process { ext.args = '-engine ncbi' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { ext.args = '-pure_helitron' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '-pure_helitron' } diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap index d53e834..9154059 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/test/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 9, + "successful tasks": 15, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,24 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "HELITRONSCANNER_DRAW": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_DRAW_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL_RC": { + "helitronscanner": "V1.1" + }, "LTRFINDER": { "LTR_FINDER_parallel": "v1.1", "ltr_finder": "v1.07" @@ -43,6 +61,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-25T13:53:22.07666" + "timestamp": "2024-11-26T22:38:20.031297" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap index a61631f..946ed5d 100644 --- a/test/nf-test/tiny/main.nf.test.snap +++ b/test/nf-test/tiny/main.nf.test.snap @@ -2,7 +2,7 @@ "tiny genome": { "content": [ { - "successful tasks": 7, + "successful tasks": 13, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,24 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "HELITRONSCANNER_DRAW": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_DRAW_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL_RC": { + "helitronscanner": "V1.1" + }, "LTRFINDER": { "LTR_FINDER_parallel": "v1.1", "ltr_finder": "v1.07" @@ -37,6 +55,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-25T13:20:57.770583" + "timestamp": "2024-11-26T22:35:05.489004" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index 357b427..cf99f9f 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -128,6 +128,10 @@ workflow EDTA { // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) + ch_helitronscanner_draw = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw + ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc + ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) + // Function: Save versions ch_versions = ch_versions From 29dbed0f0ddf8a78e524c628b889fc30fcc2eaec Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 28 Nov 2024 18:25:55 +1300 Subject: [PATCH 08/49] Added CLEANUP_TANDEM --- bin/cleanup_tandem.pl | 0 modules/local/cleanup_tandem/environment.yml | 8 +++ modules/local/cleanup_tandem/main.nf | 49 +++++++++++++ .../local/cleanup_tandem/tests/main.nf.test | 56 +++++++++++++++ .../cleanup_tandem/tests/main.nf.test.snap | 68 +++++++++++++++++++ 5 files changed, 181 insertions(+) mode change 100644 => 100755 bin/cleanup_tandem.pl create mode 100644 modules/local/cleanup_tandem/environment.yml create mode 100644 modules/local/cleanup_tandem/main.nf create mode 100644 modules/local/cleanup_tandem/tests/main.nf.test create mode 100644 modules/local/cleanup_tandem/tests/main.nf.test.snap diff --git a/bin/cleanup_tandem.pl b/bin/cleanup_tandem.pl old mode 100644 new mode 100755 diff --git a/modules/local/cleanup_tandem/environment.yml b/modules/local/cleanup_tandem/environment.yml new file mode 100644 index 0000000..8d38804 --- /dev/null +++ b/modules/local/cleanup_tandem/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::trf=4.09.1" + - "conda-forge::perl=5.32.1" \ No newline at end of file diff --git a/modules/local/cleanup_tandem/main.nf b/modules/local/cleanup_tandem/main.nf new file mode 100644 index 0000000..ae84cd2 --- /dev/null +++ b/modules/local/cleanup_tandem/main.nf @@ -0,0 +1,49 @@ +process CLEANUP_TANDEM { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'community.wave.seqera.io/library/trf_perl:44f9844b1bf765c3' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.fasta") , emit: cleaned_fasta + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + if ( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + cleanup_tandem.pl \\ + -f $fasta \\ + $args \\ + > ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/cleanup_tandem/tests/main.nf.test b/modules/local/cleanup_tandem/tests/main.nf.test new file mode 100644 index 0000000..b13870e --- /dev/null +++ b/modules/local/cleanup_tandem/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process CLEANUP_TANDEM" + script "../main.nf" + process "CLEANUP_TANDEM" + + tag "cleanup_tandem" + tag "modules_local" + tag "modules" + + test("sarscov2 - genome") { + + when { + process { + """ + input[0] = [ + [ id: 'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - genome - stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/local/cleanup_tandem/tests/main.nf.test.snap b/modules/local/cleanup_tandem/tests/main.nf.test.snap new file mode 100644 index 0000000..a36d60e --- /dev/null +++ b/modules/local/cleanup_tandem/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - genome - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ], + "cleaned_fasta": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-28T16:12:53.161124" + }, + "sarscov2 - genome": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,e73599798195a519ba2565c3f0275b93" + ] + ], + "1": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ], + "cleaned_fasta": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,e73599798195a519ba2565c3f0275b93" + ] + ], + "versions": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-28T16:12:48.160979" + } +} \ No newline at end of file From d43a72d7bca49876ef2cce2ec4be0bdcbaaa2468 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 21 Nov 2024 11:51:55 +1300 Subject: [PATCH 09/49] Initial try on format_helitronscanner --- .../format_helitronscanner/environment.yml | 7 +++ modules/local/format_helitronscanner/main.nf | 55 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 modules/local/format_helitronscanner/environment.yml create mode 100644 modules/local/format_helitronscanner/main.nf diff --git a/modules/local/format_helitronscanner/environment.yml b/modules/local/format_helitronscanner/environment.yml new file mode 100644 index 0000000..d2f633e --- /dev/null +++ b/modules/local/format_helitronscanner/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner/main.nf b/modules/local/format_helitronscanner/main.nf new file mode 100644 index 0000000..9d41ab6 --- /dev/null +++ b/modules/local/format_helitronscanner/main.nf @@ -0,0 +1,55 @@ +process FORMAT_HELITRONSCANNER_OUT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1': + 'biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" + + input: + tuple val(meta), path(genome) + path hel_fa // HelitronScanner.draw.hel.fa file + path rc_hel_fa // HelitronScanner.draw.rc.hel.fa file + + output: + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.tabout"), emit: filtered_tabout + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.fa"), emit: filtered_fa, optional: true + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.ext.fa"), emit: filtered_ext_fa, optional: true + tuple val(meta), path("${meta.id}.format_helitronscanner_out.log"), emit: log + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Set default values for the optional arguments + def sitefilter = task.ext.sitefilter != null ? task.ext.sitefilter : 1 + def minscore = task.ext.minscore != null ? task.ext.minscore : 12 + def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 + def extlen = task.ext.extlen != null ? task.ext.extlen : 30 + def extout = task.ext.extout != null ? task.ext.extout : 1 + def prefix = meta.id + + """ + # Create symbolic links to match expected filenames + ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa + ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa + + # Run the Perl script with the provided arguments + perl format_helitronscanner_out.pl \\ + -genome $genome \\ + -sitefilter $sitefilter \\ + -minscore $minscore \\ + -keepshorter $keepshorter \\ + -extlen $extlen \\ + -extout $extout \\ + &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) + + # Capture version information + cat <<-END_VERSIONS > versions.yml + "${task.process}": + Perl: \$(perl -v | grep 'This is perl' | awk '{print \$4}') + END_VERSIONS + """ +} From c65812d533d9b1b6f3c193e0086bc5f314e459c3 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 11:36:13 +1300 Subject: [PATCH 10/49] Make changes suggested by @GallVp --- .../environment.yml | 0 .../main.nf | 7 +++---- 2 files changed, 3 insertions(+), 4 deletions(-) rename modules/local/{format_helitronscanner => format_helitronscanner_out}/environment.yml (100%) rename modules/local/{format_helitronscanner => format_helitronscanner_out}/main.nf (91%) diff --git a/modules/local/format_helitronscanner/environment.yml b/modules/local/format_helitronscanner_out/environment.yml similarity index 100% rename from modules/local/format_helitronscanner/environment.yml rename to modules/local/format_helitronscanner_out/environment.yml diff --git a/modules/local/format_helitronscanner/main.nf b/modules/local/format_helitronscanner_out/main.nf similarity index 91% rename from modules/local/format_helitronscanner/main.nf rename to modules/local/format_helitronscanner_out/main.nf index 9d41ab6..2364644 100644 --- a/modules/local/format_helitronscanner/main.nf +++ b/modules/local/format_helitronscanner_out/main.nf @@ -29,14 +29,14 @@ process FORMAT_HELITRONSCANNER_OUT { def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 def extlen = task.ext.extlen != null ? task.ext.extlen : 30 def extout = task.ext.extout != null ? task.ext.extout : 1 - def prefix = meta.id + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' """ # Create symbolic links to match expected filenames ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa - # Run the Perl script with the provided arguments perl format_helitronscanner_out.pl \\ -genome $genome \\ -sitefilter $sitefilter \\ @@ -46,10 +46,9 @@ process FORMAT_HELITRONSCANNER_OUT { -extout $extout \\ &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) - # Capture version information cat <<-END_VERSIONS > versions.yml "${task.process}": - Perl: \$(perl -v | grep 'This is perl' | awk '{print \$4}') + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') END_VERSIONS """ } From 0492d4aadc5c33df01be745a64b4a77aabb076d8 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 11:49:23 +1300 Subject: [PATCH 11/49] Added some tests - not yet working, need the nf-test.config from the existing PR --- .../tests/environment.yml | 7 ++ .../tests/main.nf.test | 90 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 modules/local/format_helitronscanner_out/tests/environment.yml create mode 100644 modules/local/format_helitronscanner_out/tests/main.nf.test diff --git a/modules/local/format_helitronscanner_out/tests/environment.yml b/modules/local/format_helitronscanner_out/tests/environment.yml new file mode 100644 index 0000000..d2f633e --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test new file mode 100644 index 0000000..d1808cd --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process FORMAT_HELITRONSCANNER_OUT" + script "../main.nf" + process "FORMAT_HELITRONSCANNER_OUT" + + tag "modules" + tag "modules_nfcore" + tag "format_helitronscanner_out" + + test("homo_sapiens - genome_21_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.filtered_tabout, + process.out.log + process.out.versions + ).match() + }, + { assert path(process.out.filtered_tabout[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") }, + ) + } + + } + + test("sarscov2 - genome_fasta - no helitrons") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gff3, + process.out.versions + ).match() + }, + { assert path(process.out.filtered_tabout[0][1]).text.contains("predictions are reported in the following way") }, + ) + } + + } + + test("homo_sapiens - genome_fasta - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} From 28d08e007a21ed5d3bb41e66cb67b3cd1a31cb68 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 12:11:23 +1300 Subject: [PATCH 12/49] Typo --- modules/local/format_helitronscanner_out/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test index d1808cd..5745153 100644 --- a/modules/local/format_helitronscanner_out/tests/main.nf.test +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -26,7 +26,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.filtered_tabout, - process.out.log + process.out.log, process.out.versions ).match() }, From 5726e3944adde58acb631a2b3e5f438ff054798e Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 3 Dec 2024 14:33:19 +1300 Subject: [PATCH 13/49] Incorporated FORMAT_HELITRONSCANNER_OUT --- bin/format_helitronscanner_out.pl | 0 conf/modules.config | 4 ++ .../environment.yml | 2 +- .../local/format_helitronscanner_out/main.nf | 49 +++++++------- .../tests/environment.yml | 7 -- .../tests/main.nf.test | 65 ++----------------- .../tests/main.nf.test.snap | 63 ++++++++++++++++++ test/nf-test/small/main.nf.test.snap | 9 ++- test/nf-test/tiny/main.nf.test.snap | 9 ++- workflows/edta.nf | 19 ++++++ 10 files changed, 130 insertions(+), 97 deletions(-) mode change 100644 => 100755 bin/format_helitronscanner_out.pl delete mode 100644 modules/local/format_helitronscanner_out/tests/environment.yml create mode 100644 modules/local/format_helitronscanner_out/tests/main.nf.test.snap diff --git a/bin/format_helitronscanner_out.pl b/bin/format_helitronscanner_out.pl old mode 100644 new mode 100755 diff --git a/conf/modules.config b/conf/modules.config index 39b1af8..918b569 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -38,5 +38,9 @@ process { ext.prefix = { "${meta.id}.rc" } ext.args = '-pure_helitron' } + + withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { + ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' + } } \ No newline at end of file diff --git a/modules/local/format_helitronscanner_out/environment.yml b/modules/local/format_helitronscanner_out/environment.yml index d2f633e..b6205eb 100644 --- a/modules/local/format_helitronscanner_out/environment.yml +++ b/modules/local/format_helitronscanner_out/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::perl-bioperl=1.7.8" + - "conda-forge::perl=5.32.1" diff --git a/modules/local/format_helitronscanner_out/main.nf b/modules/local/format_helitronscanner_out/main.nf index 2364644..ebfe998 100644 --- a/modules/local/format_helitronscanner_out/main.nf +++ b/modules/local/format_helitronscanner_out/main.nf @@ -4,46 +4,35 @@ process FORMAT_HELITRONSCANNER_OUT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1': - 'biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0905ae7aa2a1c4135b448b49dd205b4eb370d4733b832594563ee06832ebd09/data': + 'community.wave.seqera.io/library/perl:67db1a8d53d64b14' }" input: tuple val(meta), path(genome) - path hel_fa // HelitronScanner.draw.hel.fa file - path rc_hel_fa // HelitronScanner.draw.rc.hel.fa file + path hel_fa + path rc_hel_fa output: - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.tabout"), emit: filtered_tabout - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.fa"), emit: filtered_fa, optional: true - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.ext.fa"), emit: filtered_ext_fa, optional: true - tuple val(meta), path("${meta.id}.format_helitronscanner_out.log"), emit: log - path "versions.yml", emit: versions + tuple val(meta), path("*.HelitronScanner.filtered.tabout") , emit: filtered_tabout + tuple val(meta), path("*.HelitronScanner.filtered.fa") , emit: filtered_fa , optional: true + tuple val(meta), path("*.HelitronScanner.filtered.ext.fa") , emit: filtered_ext_fa , optional: true + tuple val(meta), path("*.format_helitronscanner_out.log") , emit: log + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - // Set default values for the optional arguments - def sitefilter = task.ext.sitefilter != null ? task.ext.sitefilter : 1 - def minscore = task.ext.minscore != null ? task.ext.minscore : 12 - def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 - def extlen = task.ext.extlen != null ? task.ext.extlen : 30 - def extout = task.ext.extout != null ? task.ext.extout : 1 - def prefix = task.ext.prefix ?: "${meta.id}" - def args = task.ext.args ?: '' - + def prefix = task.ext.prefix ?: "$genome" + def args = task.ext.args ?: '' """ # Create symbolic links to match expected filenames ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa - perl format_helitronscanner_out.pl \\ + format_helitronscanner_out.pl \\ -genome $genome \\ - -sitefilter $sitefilter \\ - -minscore $minscore \\ - -keepshorter $keepshorter \\ - -extlen $extlen \\ - -extout $extout \\ + $args \\ &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) cat <<-END_VERSIONS > versions.yml @@ -51,4 +40,16 @@ process FORMAT_HELITRONSCANNER_OUT { perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "$genome" + """ + touch ${prefix}.HelitronScanner.filtered.tabout + touch ${prefix}.format_helitronscanner_out.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + END_VERSIONS + """ } diff --git a/modules/local/format_helitronscanner_out/tests/environment.yml b/modules/local/format_helitronscanner_out/tests/environment.yml deleted file mode 100644 index d2f633e..0000000 --- a/modules/local/format_helitronscanner_out/tests/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test index 5745153..864bc15 100644 --- a/modules/local/format_helitronscanner_out/tests/main.nf.test +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -5,65 +5,10 @@ nextflow_process { process "FORMAT_HELITRONSCANNER_OUT" tag "modules" - tag "modules_nfcore" + tag "modules_local" tag "format_helitronscanner_out" - test("homo_sapiens - genome_21_fasta") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.filtered_tabout, - process.out.log, - process.out.versions - ).match() - }, - { assert path(process.out.filtered_tabout[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") }, - ) - } - - } - - test("sarscov2 - genome_fasta - no helitrons") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.gff3, - process.out.versions - ).match() - }, - { assert path(process.out.filtered_tabout[0][1]).text.contains("predictions are reported in the following way") }, - ) - } - - } - - test("homo_sapiens - genome_fasta - stub") { + test("sarscov2 - genome_fasta - stub") { options '-stub' @@ -71,9 +16,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[1] = [] + input[2] = [] """ } } diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test.snap b/modules/local/format_helitronscanner_out/tests/main.nf.test.snap new file mode 100644 index 0000000..9079015 --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test.snap @@ -0,0 +1,63 @@ +{ + "sarscov2 - genome_fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.HelitronScanner.filtered.tabout:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.format_helitronscanner_out.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,250d1a5d5f60868f6cf0f17bd52edd91" + ], + "filtered_ext_fa": [ + + ], + "filtered_fa": [ + + ], + "filtered_tabout": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.HelitronScanner.filtered.tabout:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.format_helitronscanner_out.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,250d1a5d5f60868f6cf0f17bd52edd91" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-12-03T14:26:36.313536" + } +} \ No newline at end of file diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap index 9154059..5a164b2 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/test/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 15, + "successful tasks": 16, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,9 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "FORMAT_HELITRONSCANNER_OUT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, @@ -59,8 +62,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-11-26T22:38:20.031297" + "timestamp": "2024-12-03T14:20:03.748125" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap index 946ed5d..20a57ef 100644 --- a/test/nf-test/tiny/main.nf.test.snap +++ b/test/nf-test/tiny/main.nf.test.snap @@ -2,7 +2,7 @@ "tiny genome": { "content": [ { - "successful tasks": 13, + "successful tasks": 14, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,9 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "FORMAT_HELITRONSCANNER_OUT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, @@ -53,8 +56,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-11-26T22:35:05.489004" + "timestamp": "2024-12-03T14:16:25.986375" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index cf99f9f..05a6da3 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -8,6 +8,7 @@ include { ANNOSINE } from '../modules/gallvp/annosine/m include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' +include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' @@ -132,6 +133,24 @@ workflow EDTA { ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) + // MODULE: FORMAT_HELITRONSCANNER_OUT + ch_format_helitronscanner_inputs = ch_sanitized_fasta + | join(ch_helitronscanner_draw) + | join(ch_helitronscanner_draw_rc) + | multiMap { meta, fasta, draw, draw_rc -> + genome: [ meta, fasta ] + hel_fa: draw + rc_hel_fa: draw_rc + } + + FORMAT_HELITRONSCANNER_OUT ( + ch_format_helitronscanner_inputs.genome, + ch_format_helitronscanner_inputs.hel_fa, + ch_format_helitronscanner_inputs.rc_hel_fa, + ) + + ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) + // Function: Save versions ch_versions = ch_versions From 104fac34041b41a9a29d5d20f983f945fcbf27b9 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 13:21:56 +1300 Subject: [PATCH 14/49] Renamed test to tests to avoid meta.id conflicts in nf-test and added LTR_RETRIEVER_POSTPROCESS --- .github/check_binaries.sh | 12 + .github/workflows/linting.yml | 20 + .pre-commit-config.yaml | 11 + bin/EDTA_raw.pl | 761 ++++++++++++++++++ bin/setup_LTR_retriever_postprocess.sh | 26 + conf/modules.config | 10 + conf/test.config | 2 +- .../ltr_retriever_postprocess/environment.yml | 10 + .../local/ltr_retriever_postprocess/main.nf | 80 ++ .../nf-core/ltrretriever/ltrretriever/main.nf | 2 + .../ltrretriever/tests/main.nf.test.snap | 14 +- nextflow.config | 4 + nf-test.config | 2 +- {test => tests}/Alyrata.test.fa | 0 {test => tests}/Col.test.fa | 0 {test => tests}/Ler.test.fa | 0 {test => tests}/README.txt | 0 {test => tests}/genome.cds.fa | 0 {test => tests}/genome.cds.list | 0 {test => tests}/genome.exclude.bed | 0 {test => tests}/genome.fa | 0 {test => tests}/nf-test/nextflow.config | 0 {test => tests}/nf-test/small/main.nf.test | 26 +- .../nf-test/small/main.nf.test.snap | 21 +- {test => tests}/nf-test/tiny/main.nf.test | 0 .../nf-test/tiny/main.nf.test.snap | 0 workflows/edta.nf | 44 +- 27 files changed, 1027 insertions(+), 18 deletions(-) create mode 100755 .github/check_binaries.sh create mode 100644 .github/workflows/linting.yml create mode 100644 .pre-commit-config.yaml create mode 100755 bin/EDTA_raw.pl create mode 100755 bin/setup_LTR_retriever_postprocess.sh create mode 100644 modules/local/ltr_retriever_postprocess/environment.yml create mode 100644 modules/local/ltr_retriever_postprocess/main.nf rename {test => tests}/Alyrata.test.fa (100%) rename {test => tests}/Col.test.fa (100%) rename {test => tests}/Ler.test.fa (100%) rename {test => tests}/README.txt (100%) rename {test => tests}/genome.cds.fa (100%) rename {test => tests}/genome.cds.list (100%) rename {test => tests}/genome.exclude.bed (100%) rename {test => tests}/genome.fa (100%) rename {test => tests}/nf-test/nextflow.config (100%) rename {test => tests}/nf-test/small/main.nf.test (50%) rename {test => tests}/nf-test/small/main.nf.test.snap (72%) rename {test => tests}/nf-test/tiny/main.nf.test (100%) rename {test => tests}/nf-test/tiny/main.nf.test.snap (100%) diff --git a/.github/check_binaries.sh b/.github/check_binaries.sh new file mode 100755 index 0000000..79e8784 --- /dev/null +++ b/.github/check_binaries.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +set -euo pipefail + +EDTA_raw_pl_version=$(md5sum EDTA_raw.pl | cut -f1 -d' ') +bin_EDTA_raw_pl_version=$(md5sum bin/EDTA_raw.pl | cut -f1 -d' ') + +if [[ $EDTA_raw_pl_version != $bin_EDTA_raw_pl_version ]]; then + echo 'EDTA_raw.pl != bin/EDTA_raw.pl' + echo 'Please synchronize bin/EDTA_raw.pl with EDTA_raw.pl' + exit 1 +fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 0000000..03b6e41 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,20 @@ +name: linting +on: + pull_request: + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + + - name: Install pre-commit + run: pip install pre-commit + + - name: Run pre-commit + run: pre-commit run --all-files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..650f6a9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,11 @@ +repos: + - repo: local + hooks: + - id: check_binaries + name: Check binaries + language: system + entry: > + .github/check_binaries.sh + always_run: true + fail_fast: true + pass_filenames: false diff --git a/bin/EDTA_raw.pl b/bin/EDTA_raw.pl new file mode 100755 index 0000000..31c3cf0 --- /dev/null +++ b/bin/EDTA_raw.pl @@ -0,0 +1,761 @@ +#!/usr/bin/env perl +use warnings; +use strict; +use FindBin; +use File::Basename; +use File::Spec; # for obtaining the real path of a file +use Pod::Usage; + +######################################################## +##### Perform initial searches for TE candidates #### +##### Shujun Ou (shujun.ou.1@gmail.com, 07/16/2020) #### +######################################################## + +## Input: +# $genome + +## Output: +# $genome.LTR.raw.fa, $genome.LTR.intact.raw.fa, $genome.LTR.intact.raw.gff3 +# $genome.TIR.intact.fa, $genome.TIR.intact.raw.gff3 +# $genome.Helitron.intact.raw.fa, $genome.Helitron.intact.raw.gff3 +# $genome.LINE.raw.fa, $genome.SINE.raw.fa + +my $usage = "\nObtain raw TE libraries using various structure-based programs + +perl EDTA_raw.pl [options] + --genome [File] The genome FASTA + --species [rice|maize|others] Specify the species for identification + of TIR candidates. Default: others + --type [ltr|tir|helitron|line|sine|all] + Specify which type of raw TE candidates + you want to get. Default: all + --rmlib [FASTA] The RepeatModeler library, classified output. + --overwrite [0|1] If previous results are found, decide to + overwrite (1, rerun) or not (0, default). + --convert_seq_name [0|1] Convert long sequence name to <= 15 + characters and remove annotations (1, + default) or use the original (0) + --u [float] Neutral mutation rate to calculate the age of intact LTR elements. + Intact LTR age is found in this file: *EDTA_raw/LTR/*.pass.list. + Default: 1.3e-8 (per bp per year, from rice). + --genometools [path] Path to the GenomeTools program. (default: find from ENV) + --annosine [path] Path to the AnnoSINE program. (default: find from EDTA/bin) + --ltrretriever [path] Path to the LTR_retriever program. (default: find from ENV) + --blastplus [path] Path to the BLAST+ program. (default: find from ENV) + --tesorter [path] Path to the TEsorter program. (default: find from ENV) + --GRF [path] Path to the GRF program. (default: find from ENV) + --trf_path [path] Path to the TRF program. (default: find from ENV) + --mdust [path] Path to the mdust program. (default: find from ENV) + --repeatmasker [path] Path to the RepeatMasker program. (default: find from ENV) + --repeatmodeler [path] Path to the RepeatModeler2 program. (default: find from ENV) + --threads|-t [int] Number of theads to run this script. Default: 4 + --help|-h Display this help info +\n"; + +# pre-defined +my $genome = ''; +my $species = 'others'; +my $type = 'all'; +my $RMlib = 'null'; +my $overwrite = 0; #0, no rerun. 1, rerun even old results exist. +my $convert_name = 1; #0, use original seq names; 1 shorten names. +my $maxint = 5000; #maximum interval length (bp) between TIRs (for GRF in TIR-Learner) +my $miu = 1.3e-8; #mutation rate, per bp per year, from rice +my $threads = 4; +my $script_path = $FindBin::Bin; +my $cleanup_misclas = "$script_path/bin/cleanup_misclas.pl"; +my $get_range = "$script_path/bin/get_range.pl"; +my $rename_LTR = "$script_path/bin/rename_LTR_skim.pl"; +my $rename_RM = "$script_path/bin/rename_RM_TE.pl"; +my $filter_gff = "$script_path/bin/filter_gff3.pl"; +my $rename_tirlearner = "$script_path/bin/rename_tirlearner.pl"; +my $call_seq = "$script_path/bin/call_seq_by_list.pl"; +my $output_by_list = "$script_path/bin/output_by_list.pl"; +my $cleanup_tandem = "$script_path/bin/cleanup_tandem.pl"; +my $get_ext_seq = "$script_path/bin/get_ext_seq.pl"; +my $format_helitronscanner = "$script_path/bin/format_helitronscanner_out.pl"; +my $flank_filter = "$script_path/bin/flanking_filter.pl"; +my $make_bed = "$script_path/bin/make_bed_with_intact.pl"; +my $bed2gff = "$script_path/bin/bed2gff.pl"; +my $genometools = ''; #path to the genometools program +my $repeatmasker = ''; #path to the RepeatMasker program +my $repeatmodeler = ''; #path to the RepeatModeler program +my $LTR_retriever = ''; #path to the LTR_retriever program +my $TEsorter = ''; #path to the TEsorter program +my $blastplus = ''; #path to the blastn program +my $mdust = ''; #path to mdust +my $trf = ''; #path to trf +my $GRF = ''; #path to GRF +my $annosine = ""; #path to the AnnoSINE program + +# my $TIR_Learner = "$script_path/bin/TIR-Learner3/"; #tianyulu +# my $LTR_FINDER = "$script_path/bin/LTR_FINDER_parallel/LTR_FINDER_parallel"; #tianyulu +# my $LTR_HARVEST = "$script_path/bin/LTR_HARVEST_parallel/LTR_HARVEST_parallel"; #tianyulu +my $HelitronScanner_Runner = "$script_path/bin/run_helitron_scanner.sh"; + +my $TIR_Learner = ""; #path to TIR-Learner3 program #tianyulu +my $LTR_FINDER = ""; #path to LTR_FINDER_parallel program #tianyulu +my $LTR_HARVEST = ""; #path to LTR_HARVEST_parallel program #tianyulu +my $HelitronScanner = ""; #path to HelitronScanner program #tianyulu + +my $help = undef; + +# read parameters +my $k=0; +foreach (@ARGV){ + $genome = $ARGV[$k+1] if /^--genome$/i and $ARGV[$k+1] !~ /^-/; + $species = $ARGV[$k+1] if /^--species$/i and $ARGV[$k+1] !~ /^-/; + $type = lc $ARGV[$k+1] if /^--type$/i and $ARGV[$k+1] !~ /^-/; + $RMlib = $ARGV[$k+1] if /^--rmlib$/i and $ARGV[$k+1] !~ /^-/; + $overwrite = $ARGV[$k+1] if /^--overwrite$/i and $ARGV[$k+1] !~ /^-/; + $convert_name = $ARGV[$k+1] if /^--convert_seq_name$/i and $ARGV[$k+1] !~ /^-/; + $miu = $ARGV[$k+1] if /^--u$/i and $ARGV[$k+1] !~ /^-/; + $genometools = $ARGV[$k+1] if /^--genometools/i and $ARGV[$k+1] !~ /^-/; + $repeatmasker = $ARGV[$k+1] if /^--repeatmasker$/i and $ARGV[$k+1] !~ /^-/; + $repeatmodeler = $ARGV[$k+1] if /^--repeatmodeler$/i and $ARGV[$k+1] !~ /^-/; + $annosine = $ARGV[$k+1] if /^--annosine$/i and $ARGV[$k+1] !~ /^-/; + $LTR_retriever = $ARGV[$k+1] if /^--ltrretriever/i and $ARGV[$k+1] !~ /^-/; + $TEsorter = $ARGV[$k+1] if /^--tesorter$/i and $ARGV[$k+1] !~ /^-/; + $blastplus = $ARGV[$k+1] if /^--blastplus$/i and $ARGV[$k+1] !~ /^-/; + $mdust = $ARGV[$k+1] if /^--mdust$/i and $ARGV[$k+1] !~ /^-/; + $trf = $ARGV[$k+1] if /^--trf_path$/i and $ARGV[$k+1] !~ /^-/; + $GRF = $ARGV[$k+1] if /^--GRF$/i and $ARGV[$k+1] !~ /^-/; + $threads = $ARGV[$k+1] if /^--threads$|^-t$/i and $ARGV[$k+1] !~ /^-/; + $help = 1 if /^--help$|^-h$/i; + $k++; + } + +# check files and parameters +if ($help){ + pod2usage( { + -verbose => 0, + -exitval => 0, + -message => "$usage\n" } ); + } + +if (!-s $genome){ + pod2usage( { + -message => "At least 1 parameter is required:\n1) Input fasta file: --genome\n". + "\n$usage\n\n", + -verbose => 0, + -exitval => 2 } ); + } + +if ($species){ + $species =~ s/rice/Rice/i; + $species =~ s/maize/Maize/i; + $species =~ s/others/others/i; + die "The expected value for the species parameter is Rice or Maize or others!\n" unless $species eq "Rice" or $species eq "Maize" or $species eq "others"; + } + +die "The expected value for the type parameter is ltr or tir or helitron or all!\n" unless $type eq "ltr" or $type eq "line" or $type eq "tir" or $type eq "helitron" or $type eq "sine" or $type eq "all"; + +# check bolean +if ($overwrite != 0 and $overwrite != 1){ die "The expected value for the overwrite parameter is 0 or 1!\n"}; +if ($convert_name != 0 and $convert_name != 1){ die "The expected value for the convert_seq_name parameter is 0 or 1!\n"}; +if ($threads !~ /^[0-9]+$/){ die "The expected value for the threads parameter is an integer!\n"}; +if ($miu !~ /[0-9\.e\-]+/){ die "The expected value for the u parameter is float value without units!\n"} + +chomp (my $date = `date`); +print STDERR "$date\tEDTA_raw: Check dependencies, prepare working directories.\n\n"; + +# check files and dependencies +# die "The LTR_FINDER_parallel is not found in $LTR_FINDER!\n" unless -s $LTR_FINDER; #tianyulu +# die "The LTR_HARVEST_parallel is not found in $LTR_HARVEST!\n" unless -s $LTR_HARVEST; #tianyulu +# die "The TIR_Learner is not found in $TIR_Learner!\n" unless -s "$TIR_Learner/bin/main.py"; #tianyulu +die "The script get_range.pl is not found in $get_range!\n" unless -s $get_range; +die "The script rename_LTR_skim.pl is not found in $rename_LTR!\n" unless -s $rename_LTR; +die "The script filter_gff3.pl is not found in $filter_gff!\n" unless -s $filter_gff; +die "The script call_seq_by_list.pl is not found in $call_seq!\n" unless -s $call_seq; +die "The script output_by_list.pl is not found in $output_by_list!\n" unless -s $output_by_list; +die "The script rename_tirlearner.pl is not found in $rename_tirlearner!\n" unless -s $rename_tirlearner; +die "The script cleanup_tandem.pl is not found in $cleanup_tandem!\n" unless -s $cleanup_tandem; +die "The script get_ext_seq.pl is not found in $get_ext_seq!\n" unless -s $get_ext_seq; +# die "The HelitronScanner is not found in $HelitronScanner!\n" unless -s $HelitronScanner; #tianyulu +die "The script format_helitronscanner_out.pl is not found in $format_helitronscanner!\n" unless -s $format_helitronscanner; +die "The script flanking_filter.pl is not found in $flank_filter!\n" unless -s $flank_filter; +die "The script bed2gff.pl is not found in $bed2gff!\n" unless -s $bed2gff; +die "The script make_bed_with_intact.pl is not found in $make_bed!\n" unless -s $make_bed; + +# GenomeTools +chomp ($genometools=`command -v gt 2>/dev/null`) if $genometools eq ''; +$genometools =~ s/\s+$//; +$genometools = dirname($genometools) unless -d $genometools; +$genometools="$genometools/" if $genometools ne '' and $genometools !~ /\/$/; +die "Error: gt is not found in the genometools path $genometools!\n" unless -X "${genometools}gt"; +# RepeatMasker +my $rand=int(rand(1000000)); +chomp ($repeatmasker=`command -v RepeatMasker 2>/dev/null`) if $repeatmasker eq ''; +$repeatmasker =~ s/\s+$//; +$repeatmasker = dirname($repeatmasker) unless -d $repeatmasker; +$repeatmasker="$repeatmasker/" if $repeatmasker ne '' and $repeatmasker !~ /\/$/; +die "Error: RepeatMasker is not found in the RepeatMasker path $repeatmasker!\n" unless -X "${repeatmasker}RepeatMasker"; +# `cp $script_path/database/dummy060817.fa ./dummy060817.fa.$rand`; +`cp \"$script_path/database/dummy060817.fa\" ./dummy060817.fa.$rand`; #tianyulu +my $RM_test=`${repeatmasker}RepeatMasker -e ncbi -q -pa 1 -no_is -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand 2>/dev/null`; +die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/done//gi; +`rm dummy060817.fa.$rand*`; +# RepeatModeler +chomp ($repeatmodeler=`command -v RepeatModeler 2>/dev/null`) if $repeatmodeler eq ''; +$repeatmodeler =~ s/\s+$//; +$repeatmodeler = dirname($repeatmodeler) unless -d $repeatmodeler; +$repeatmodeler="$repeatmodeler/" if $repeatmodeler ne '' and $repeatmodeler !~ /\/$/; +die "Error: RepeatModeler is not found in the RepeatModeler path $repeatmodeler!\n" unless -X "${repeatmodeler}RepeatModeler"; +# AnnoSINE +chomp ($annosine=`command -v AnnoSINE_v2 2>/dev/null`) if $annosine eq ''; +$annosine =~ s/\s+$//; +$annosine = dirname($annosine) unless -d $annosine; +$annosine="$annosine/" if $annosine ne '' and $annosine !~ /\/$/; +die "Error: AnnoSINE is not found in the AnnoSINE path $annosine!\n" unless (-X "${annosine}AnnoSINE_v2"); +# LTR_retriever +chomp ($LTR_retriever=`command -v LTR_retriever 2>/dev/null`) if $LTR_retriever eq ''; +$LTR_retriever =~ s/\s+$//; +$LTR_retriever = dirname($LTR_retriever) unless -d $LTR_retriever; +$LTR_retriever="$LTR_retriever/" if $LTR_retriever ne '' and $LTR_retriever !~ /\/$/; +die "Error: LTR_retriever is not found in the LTR_retriever path $LTR_retriever!\n" unless -X "${LTR_retriever}LTR_retriever"; +# TEsorter +chomp ($TEsorter=`command -v TEsorter 2>/dev/null`) if $TEsorter eq ''; +$TEsorter =~ s/\s+$//; +$TEsorter = dirname($TEsorter) unless -d $TEsorter; +$TEsorter="$TEsorter/" if $TEsorter ne '' and $TEsorter !~ /\/$/; +die "Error: TEsorter is not found in the TEsorter path $TEsorter!\n" unless -X "${TEsorter}TEsorter"; +# makeblastdb, blastn +chomp ($blastplus=`command -v makeblastdb 2>/dev/null`) if $blastplus eq ''; +$blastplus =~ s/\s+$//; +$blastplus = dirname($blastplus) unless -d $blastplus; +$blastplus="$blastplus/" if $blastplus ne '' and $blastplus !~ /\/$/; +die "Error: makeblastdb is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}makeblastdb"; +die "Error: blastn is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}blastn"; +# mdust +chomp ($mdust=`command -v mdust 2>/dev/null`) if $mdust eq ''; +$mdust =~ s/\s+$//; +$mdust = dirname($mdust) unless -d $mdust; +$mdust = "$mdust/" if $mdust ne '' and $mdust !~ /\/$/; +die "Error: mdust is not found in the mdust path $mdust!\n" unless -X "${mdust}mdust"; +# trf +chomp ($trf=`command -v trf 2>/dev/null`) if $trf eq ''; +$trf=~s/\n$//; +`$trf 2>/dev/null`; +die "Error: Tandem Repeat Finder is not found in the TRF path $trf!\n" if $?==32256; +# GRF +chomp ($GRF = `command -v grf-main 2>/dev/null`) if $GRF eq ''; +$GRF =~ s/\n$//; +my $grfp= dirname ($GRF); +$grfp =~ s/\n$//; +`${grfp}grf-main 2>/dev/null`; +die "Error: The Generic Repeat Finder (GRF) is not found in the GRF path: $grfp\n" if $?==32256; + +# # TIR-Learner3 +# chomp ($TIR_Learner = `which TIR-Learner 2>/dev/null`) if $TIR_Learner eq ''; +# $TIR_Learner =~ s/\n$//; +# my $tirp= dirname ($TIR_Learner); +# $tirp =~ s/\n$//; +# `${tirp}TIR-Learner 2>/dev/null`; +# die "Error: TIR-Learner3 is not found in the TIR-Learner path: $tirp\n" if $?==32256; + +# TIR-Learner #tianyuLu +# Remove any trailing whitespace +$TIR_Learner =~ s/\s+$//; +if ($TIR_Learner eq "") { + # Find TIR-Learner path and remove any trailing newline + chomp ($TIR_Learner=`command -v TIR-Learner 2>/dev/null`); + die "Error: TIR-Learner not installed!\n" if $TIR_Learner eq ""; + # $TIR_Learner =~ s/\s+$//; +} else { + # # Extract directory name from path if path is not a directory + # $TIR_Learner = dirname($TIR_Learner) unless -d $TIR_Learner; + # If path is directory + if (-d $TIR_Learner) { + # # Add trailing slash if path not empty string and not already end with slash + # $TIR_Learner .= "/" if $TIR_Learner ne "" and $TIR_Learner !~ /\/$/; + # Add trailing slash if path not already end with slash + $TIR_Learner .= "/" if $TIR_Learner !~ /\/$/; + $TIR_Learner = "python3 $TIR_Learner/TIR-Learner.py"; + } +} +`$TIR_Learner 2>/dev/null`; +die "Error: TIR-Learner is not found in the path $TIR_Learner!\n" if $?==32256 || $?==2; + +# LTR_FINDER_parallel #tianyuLu +$LTR_FINDER =~ s/\s+$//; +if ($LTR_FINDER eq "") { + chomp ($LTR_FINDER=`command -v LTR_FINDER_parallel 2>/dev/null`); + die "Error: LTR_FINDER_parallel not installed!\n" if $LTR_FINDER eq ""; +} else { + if (-d $LTR_FINDER) { + $LTR_FINDER .= "/" if $LTR_FINDER !~ /\/$/; + $LTR_FINDER = "perl $LTR_FINDER/LTR_FINDER_parallel"; + } +} +`$LTR_FINDER 2>/dev/null`; +die "Error: LTR_FINDER_parallel is not found in the path $LTR_FINDER!\n" if $?==32256 || $?==2; + +# LTR_HARVEST_parallel #tianyuLu +$LTR_HARVEST =~ s/\s+$//; +if ($LTR_HARVEST eq "") { + chomp ($LTR_HARVEST=`command -v LTR_HARVEST_parallel 2>/dev/null`); + die "Error: LTR_HARVEST_parallel not installed!\n" if $LTR_HARVEST eq ""; +} else { + if (-d $LTR_HARVEST) { + $LTR_HARVEST .= "/" if $LTR_HARVEST !~ /\/$/; + $LTR_HARVEST = "perl $LTR_HARVEST/LTR_HARVEST_parallel"; + } +} +`$LTR_HARVEST 2>/dev/null`; +die "Error: LTR_HARVEST_parallel is not found in the path $LTR_HARVEST!\n" if $?==32256 || $?==2; + +# HelitronScanner #tianyuLu +$HelitronScanner =~ s/\s+$//; +if ($HelitronScanner eq "") { + chomp ($HelitronScanner=`command -v HelitronScanner 2>/dev/null`); + die "Error: HelitronScanner not installed!\n" if $HelitronScanner eq ""; +} else { + if (-d $HelitronScanner) { + $HelitronScanner .= "/" if $HelitronScanner !~ /\/$/; + } +} + +# make a softlink to the genome +my $genome_file = basename($genome); +`ln -s $genome $genome_file` unless -e $genome_file; +$genome = $genome_file; + +# check $RMlib +if ($RMlib ne 'null'){ + if (-e $RMlib){ + print "\tA RepeatModeler library $RMlib is provided via --rmlib. Please make sure this is a RepeatModeler2 generated and classified library (some levels of unknown classification is OK).\n\n"; + chomp ($RMlib = `realpath $RMlib`); + `ln -s $RMlib $genome.RM2.raw.fa` unless -s "$genome.RM2.raw.fa"; + $RMlib = "$genome.RM2.raw.fa"; + } else { + die "\tERROR: The RepeatModeler library $RMlib you specified is not found!\n\n"; + } + } + +# check if duplicated sequences found +my $id_mode = 0; #record the mode of id conversion. +my $id_len = `grep \\> $genome|perl -ne 'chomp; s/>//g; my \$len=length \$_; \$max=\$len if \$max<\$len; print "\$max\\n"'`; #find out the longest sequence ID length in the genome +$id_len =~ s/\s+$//; +$id_len = (split /\s+/, $id_len)[-1]; +my $raw_id = `grep \\> $genome|wc -l`; +my $old_id = `grep \\> $genome|sort -u|wc -l`; +if ($raw_id > $old_id){ + chomp ($date = `date`); + die "$date\tERROR: Identical sequence IDs found in the provided genome! Please resolve this issue and try again.\n"; + } + +if ($convert_name == 1){ +if (-s "$genome.mod"){ + $genome = "$genome.mod"; + } else { + +# remove sequence annotations (content after the first space in sequence names) and replace special characters with _, convert non-ATGC bases into Ns +`perl -nle 'my \$info=(split)[0]; \$info=~s/[\\~!@#\\\$%\\^&\\*\\(\\)\\+\\\-\\=\\?\\[\\]\\{\\}\\:;",\\<\\/\\\\\|]+/_/g; \$info=~s/_+/_/g; \$info=~s/[^ATGCN]/N/gi unless /^>/; print \$info' $genome > $genome.$rand.mod`; + +# try to shortern sequences +my $id_len_max = 13; # allowed longest length of a sequence ID in the input file +if ($id_len > $id_len_max){ + chomp ($date = `date`); + print "$date\tThe longest sequence ID in the genome contains $id_len characters, which is longer than the limit ($id_len_max)\n"; + print "\tTrying to reformat seq IDs...\n\t\tAttempt 1...\n"; + `perl -lne 'chomp; if (s/^>+//) {s/^\\s+//; \$_=(split)[0]; s/(.{1,$id_len_max}).*/>\$1/g;} print "\$_"' $genome.$rand.mod > $genome.$rand.temp`; + my $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + chomp ($date = `date`); + if ($old_id == $new_id){ + $id_mode = 1; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + print "\t\tAttempt 2...\n"; + `perl -ne 'chomp; if (/^>/) {\$_=">\$1" if /([0-9]+)/;} print "\$_\n"' $genome.$rand.mod > $genome.$rand.temp`; + $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + if ($old_id == $new_id){ + $id_mode = 2; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + `rm $genome.$rand.temp $genome.$rand.mod 2>/dev/null`; + die "$date\tERROR: Fail to convert seq IDs to <= $id_len_max characters! Please provide a genome with shorter seq IDs.\n\n"; + } + } + } else { + `mv $genome.$rand.mod $genome.mod`; + } +$genome = "$genome.mod"; +} +} + +# Make working directories +`mkdir $genome.EDTA.raw` unless -e "$genome.EDTA.raw" && -d "$genome.EDTA.raw"; +`mkdir $genome.EDTA.raw/LTR` unless -e "$genome.EDTA.raw/LTR" && -d "$genome.EDTA.raw/LTR"; +`mkdir $genome.EDTA.raw/SINE` unless -e "$genome.EDTA.raw/SINE" && -d "$genome.EDTA.raw/SINE"; +`mkdir $genome.EDTA.raw/LINE` unless -e "$genome.EDTA.raw/LINE" && -d "$genome.EDTA.raw/LINE"; +`mkdir $genome.EDTA.raw/TIR` unless -e "$genome.EDTA.raw/TIR" && -d "$genome.EDTA.raw/TIR"; +`mkdir $genome.EDTA.raw/Helitron` unless -e "$genome.EDTA.raw/Helitron" && -d "$genome.EDTA.raw/Helitron"; + + +########################### +###### LTR_retriever ###### +########################### + +if ($type eq "ltr" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find LTR candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/LTR"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and -s "$genome.LTR.raw.fa"){ + print STDERR "$date\tExisting result file $genome.LTR.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify LTR retrotransposon candidates from scratch.\n\n"; + +# run LTRharvest +if ($overwrite eq 0 and -s "$genome.harvest.combine.scn"){ + print STDERR "$date\tExisting raw result $genome.harvest.scn found!\n\t\tWill use this for further analyses.\n\n"; + } else { + # `perl $LTR_HARVEST -seq $genome -threads $threads -gt $genometools -size 1000000 -time 300`; + `$LTR_HARVEST -seq $genome -threads $threads -gt $genometools -size 1000000 -time 300`; #tianyulu + } + +# run LTR_FINDER_parallel +if ($overwrite eq 0 and -s "$genome.finder.combine.scn"){ + print STDERR "$date\tExisting raw result $genome.finder.combine.scn found!\n\t\tWill use this for further analyses.\n\n"; + } else { + # `perl $LTR_FINDER -seq $genome -threads $threads -harvest_out -size 1000000 -time 300`; + `$LTR_FINDER -seq $genome -threads $threads -harvest_out -size 1000000 -time 300`; #tianyulu + } + +# run LTR_retriever +if ($overwrite eq 0 and -s "$genome.LTRlib.fa"){ + print STDERR "$date\tExisting LTR_retriever result $genome.LTRlib.fa found!\n\t\tWill use this for further analyses.\n\n"; + } else { + `cat $genome.harvest.combine.scn $genome.finder.combine.scn > $genome.rawLTR.scn`; + `${LTR_retriever}LTR_retriever -genome $genome -inharvest $genome.rawLTR.scn -u $miu -threads $threads -noanno -trf_path $trf -blastplus $blastplus -repeatmasker $repeatmasker`; + } + +# get full-length LTR from pass.list +`awk '{if (\$1 !~ /#/) print \$1"\\t"\$1}' $genome.pass.list | perl $call_seq - -C $genome > $genome.LTR.intact.fa.ori`; +`perl -i -nle 's/\\|.*//; print \$_' $genome.LTR.intact.fa.ori`; +`perl $rename_LTR $genome.LTR.intact.fa.ori $genome.defalse > $genome.LTR.intact.fa.anno`; +`mv $genome.LTR.intact.fa.anno $genome.LTR.intact.fa.ori`; + +# remove simple repeats and candidates with simple repeats at terminals +`${mdust}mdust $genome.LTR.intact.fa.ori > $genome.LTR.intact.fa.ori.dusted`; +`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 100 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.LTR.intact.fa.ori.dusted > $genome.LTR.intact.fa.ori.dusted.cln`; + +# annotate and remove not LTR candidates +`${TEsorter}TEsorter $genome.LTR.intact.fa.ori.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; +`perl $cleanup_misclas $genome.LTR.intact.fa.ori.dusted.cln.rexdb.cls.tsv`; +`mv $genome.LTR.intact.fa.ori.dusted.cln.cln $genome.LTR.intact.raw.fa`; +`mv $genome.LTR.intact.fa.ori.dusted.cln.cln.list $genome.LTR.intact.raw.fa.anno.list`; +`cp $genome.LTR.intact.raw.fa.anno.list ../`; + +# generate annotated output and gff +`perl $output_by_list 1 $genome.LTR.intact.fa.ori 1 $genome.LTR.intact.raw.fa -FA -ex|grep \\>|perl -nle 's/>//; print "Name\\t\$_"' > $genome.LTR.intact.fa.ori.rmlist`; +`perl $filter_gff $genome.pass.list.gff3 $genome.LTR.intact.fa.ori.rmlist | perl -nle 's/LTR_retriever/EDTA/gi; print \$_' > $genome.LTR.intact.raw.gff3`; +`rm $genome`; + } + +# copy result files out +`touch $genome.LTRlib.fa` unless -e "$genome.LTRlib.fa"; +`cp $genome.LTRlib.fa $genome.LTR.raw.fa`; +`cp $genome.LTRlib.fa ../$genome.LTR.raw.fa`; +`cp $genome.LTR.intact.raw.fa $genome.LTR.intact.raw.gff3 ../ 2>/dev/null`; +`cp $genome.LTR.intact.fa ../$genome.LTR.intact.raw.fa` if -s "$genome.LTR.intact.fa"; +`cp $genome.LTR.intact.gff3 ../$genome.LTR.intact.raw.gff3` if -s "$genome.LTR.intact.gff3"; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: LTR results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.LTR.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.LTR.raw.fa"){ + print STDERR "$date\tFinish finding LTR candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The LTR result file has 0 bp!\n\n"; + } + +} + + +############################# +###### AnnoSINE ###### +############################# +if ($type eq "sine" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find SINE candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/SINE"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Remove existing results +`rm -rf Seed_SINE.fa Step* HMM_out 2>/dev/null` if $overwrite eq 1; + +# run AnnoSINE_v2 +my $status; # record status of AnnoSINE execution +if (-s "Seed_SINE.fa"){ + print STDERR "$date\tExisting result file Seed_SINE.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun AnnoSINE_v2.\n\n"; + } else { + $status = system("python3 ${annosine}AnnoSINE_v2 -t $threads -a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1 3 $genome ./ > /dev/null 2>&1"); + } + +# filter and reclassify AnnoSINE candidates with TEsorter and make SINE library +if (-s "Seed_SINE.fa"){ + # annotate and remove non-SINE candidates + `awk '{gsub(/Unknown/, "unknown"); print \$1}' Seed_SINE.fa > $genome.AnnoSINE.raw.fa`; + `${TEsorter}TEsorter $genome.AnnoSINE.raw.fa --disable-pass2 -p $threads 2>/dev/null`; + `touch $genome.AnnoSINE.raw.fa.rexdb.cls.tsv` unless -e "$genome.AnnoSINE.raw.fa.rexdb.cls.tsv"; + `perl $cleanup_misclas $genome.AnnoSINE.raw.fa.rexdb.cls.tsv`; + + # clean up tandem repeat + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.AnnoSINE.raw.fa.cln > $genome.SINE.raw.fa`; + } +elsif ($status == 0) { + print "\t\tAnnoSINE is finished without error, but the Seed_SINE.fa file is not produced.\n\n"; + `touch $genome.SINE.raw.fa`; + } +else { + print "\t\tAnnoSINE exited with error, please test run AnnoSINE to make sure it's working.\n\n"; + } + +# copy result files out +`cp $genome.SINE.raw.fa ../`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: SINE results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.SINE.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.SINE.raw.fa"){ + print STDERR "$date\tFinish finding SINE candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The SINE result file has 0 bp!\n\n"; + } + +} + + +############################# +###### RepeatModeler ###### +############################# + +if ($type eq "line" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find LINE candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/LINE"; +`ln -s ../../$genome $genome` unless -s $genome; +`cp ../../$RMlib $RMlib` if $RMlib ne 'null'; + +# Try to recover existing results or run RepeatModeler2 +chomp ($date = `date`); +if ($overwrite eq 0 and -s $RMlib){ + if (-s "$genome-families.fa"){ + print STDERR "$date\tExisting result file $genome-families.fa found!\n\t\tWill not use the provided RepeatModeler2 library since --overwrite 0.\n\t\tPlease specify --overwrite 1 if you want to use the provided --rmlib file.\n\n"; + } else { + `cp $RMlib "$genome-families.fa" 2>/dev/null`; + } + } + +if ($overwrite eq 0 and -s "$genome-families.fa"){ + print STDERR "$date\tExisting result file $genome-families.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + # run RepeatModeler2 + print STDERR "$date\tIdentify LINE retrotransposon candidates from scratch.\n\n"; + my $status; # record status of RepeatModeler execution + `${repeatmodeler}BuildDatabase -name $genome $genome`; + $status = system("${repeatmodeler}RepeatModeler -engine ncbi -threads $threads -database $genome > repeatmodeler.log 2>&1"); + if ($status != 0) { + # Execute the old version of RepeatModeler + $status = system("${repeatmodeler}RepeatModeler -engine ncbi -pa $threads -database $genome > repeatmodeler.log 2>&1"); + print "ERROR: RepeatModeler did not run correctly. Please test run this command: + ${repeatmodeler}RepeatModeler -engine ncbi -pa $threads -database $genome + " and exit unless $status == 0; + } + `rm $genome.nhr $genome.nin $genome.nnd $genome.nni $genome.nog $genome.nsq $genome.njs $genome.translation 2>/dev/null`; + } + +# filter and reclassify RepeatModeler candidates with TEsorter and make LINE library +if (-s "$genome-families.fa"){ + # annotate and remove misclassified candidates + `awk '{gsub(/Unknown/, "unknown"); print \$1}' $genome-families.fa > $genome.RM2.raw.fa` if -e "$genome-families.fa"; + `${TEsorter}TEsorter $genome.RM2.raw.fa --disable-pass2 -p $threads 2>/dev/null`; + `perl $cleanup_misclas $genome.RM2.raw.fa.rexdb.cls.tsv`; + + # reclassify clean candidates + `${TEsorter}TEsorter $genome.RM2.raw.fa.cln --disable-pass2 -p $threads 2>/dev/null`; + `perl -nle 's/>\\S+\\s+/>/; print \$_' $genome.RM2.raw.fa.cln.rexdb.cls.lib > $genome.RM2.raw.fa.cln`; + + # clean up tandem repeat + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.RM2.raw.fa.cln > $genome.RM2.raw.fa.cln2`; + `grep -P 'LINE|SINE' $genome.RM2.raw.fa.cln2 | perl $output_by_list 1 $genome.RM2.raw.fa.cln2 1 - -FA > $genome.LINE.raw.fa`; + `grep -P 'LINE|SINE' $genome.RM2.raw.fa.cln2 | perl $output_by_list 1 $genome.RM2.raw.fa.cln2 1 - -FA -ex > $genome.RM2.fa`; + } else { + print "\t\tRepeatModeler is finished, but the $genome-families.fa file is not produced.\n\n"; + `touch $genome.RM2.raw.fa $genome.LINE.raw.fa $genome.RM2.fa`; + } + +# copy result files out +`cp $genome.LINE.raw.fa $genome.RM2.fa ../`; #update the filtered RM2 result in the EDTA/raw folder +`cp $genome.RM2.raw.fa ../../`; #update the raw RM2 result in the EDTA folder +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: LINE results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.LINE.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.LINE.raw.fa"){ + print STDERR "$date\tFinish finding LINE candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The LINE result file has 0 bp!\n\n"; + } +} + + +########################### +###### TIR-Learner ###### +########################### + +if ($type eq "tir" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find TIR candidates.\n\n"; + +# pre-set parameters +my $genome_file_real_path=File::Spec->rel2abs($genome); # the genome file with real path + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/TIR"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and (-s "$genome.TIR.intact.raw.fa" or -s "$genome.TIR.intact.fa")){ + print STDERR "$date\tExisting result file $genome.TIR.intact.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify TIR candidates from scratch.\n\n"; + print STDERR "Species: $species\n"; + + # run TIR-Learner + if ($overwrite eq 0 and -s "./TIR-Learner-Result/TIR-Learner_FinalAnn.fa"){ + print STDERR "$date\tExisting raw result TIR-Learner_FinalAnn.fa found!\n\t\tWill use this for further analyses.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + `$TIR_Learner -f $genome_file_real_path -s $species -t $threads -l $maxint -c -o $genome_file_real_path.EDTA.raw/TIR --grf_path $grfp --gt_path $genometools`; #TianyuLu + } + + # clean raw predictions with flanking alignment + `perl $rename_tirlearner ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa | perl -nle 's/TIR-Learner_//g; print \$_' > $genome.TIR`; + `perl $get_ext_seq $genome $genome.TIR`; + `perl $flank_filter -genome $genome -query $genome.TIR.ext30.fa -miniden 90 -mincov 0.9 -maxct 20 -blastplus $blastplus -t $threads`; + + # recover superfamily info + `perl $output_by_list 1 $genome.TIR 1 $genome.TIR.ext30.fa.pass.fa -FA -MSU0 -MSU1 > $genome.TIR.ext30.fa.pass.fa.ori`; + + # remove simple repeats and candidates with simple repeats at terminals + `${mdust}mdust $genome.TIR.ext30.fa.pass.fa.ori > $genome.TIR.ext30.fa.pass.fa.dusted`; + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.TIR.ext30.fa.pass.fa.dusted > $genome.TIR.ext30.fa.pass.fa.dusted.cln`; + + # annotate and remove non-TIR candidates + `${TEsorter}TEsorter $genome.TIR.ext30.fa.pass.fa.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; + `perl $cleanup_misclas $genome.TIR.ext30.fa.pass.fa.dusted.cln.rexdb.cls.tsv`; + `mv $genome.TIR.ext30.fa.pass.fa.dusted.cln.cln $genome.TIR.intact.raw.fa`; + `cp $genome.TIR.ext30.fa.pass.fa.dusted.cln.cln.list $genome.TIR.intact.raw.fa.anno.list`; + `cp $genome.TIR.intact.raw.fa.anno.list ../`; + + # get gff3 of intact TIR elements + `perl -nle 's/\\-\\+\\-/_Len:/; my (\$chr, \$method, \$supfam, \$s, \$e, \$anno) = (split)[0,1,2,3,4,8]; my \$class='DNA'; \$class='MITE' if \$e-\$s+1 <= 600; my (\$tir, \$iden, \$tsd)=(\$1, \$2/100, \$3) if \$anno=~/TIR:(.*)_([0-9.]+)_TSD:([a-z0-9._]+)_LEN/i; print "\$chr \$s \$e \$chr:\$s..\$e \$class/\$supfam structural \$iden . . . TSD=\$tsd;TIR=\$tir"' ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3 | perl $output_by_list 4 - 1 $genome.TIR.intact.raw.fa -MSU0 -MSU1 > $genome.TIR.intact.raw.bed`; + `perl $bed2gff $genome.TIR.intact.raw.bed TIR > $genome.TIR.intact.raw.gff3`; + } + +# copy result files out +`cp $genome.TIR.intact.bed ../$genome.TIR.intact.raw.bed` if -s "$genome.TIR.intact.bed"; # recover /dev/null`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: TIR results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.TIR.intact.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.TIR.intact.raw.fa"){ + print STDERR "$date\tFinish finding TIR candidates.\n\n"; + } else { + print STDERR "Warning: The TIR result file has 0 bp!\n\n"; + } + +} + + +############################# +###### HelitronScanner ###### +############################# + +if ($type eq "helitron" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find Helitron candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/Helitron"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and (-s "$genome.Helitron.intact.raw.fa" or -s "$genome.Helitron.intact.fa")){ + print STDERR "$date\tExisting result file $genome.Helitron.intact.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify Helitron candidates from scratch.\n\n"; + +# run HelitronScanner +`$HelitronScanner_Runner $genome $threads \"$HelitronScanner\"`; + +# filter candidates based on repeatness of flanking regions +`perl $format_helitronscanner -genome $genome -sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1`; +`perl $flank_filter -genome $genome -query $genome.HelitronScanner.filtered.ext.fa -miniden 90 -mincov 0.9 -maxct 5 -blastplus $blastplus -t $threads`; #more relaxed +#`perl $flank_filter -genome $genome -query $genome.HelitronScanner.filtered.ext.fa -miniden 80 -mincov 0.8 -maxct 5 -blastplus $blastplus -t $threads`; #more stringent + +# remove simple repeats and candidates with simple repeats at terminals +`perl $output_by_list 1 $genome.HelitronScanner.filtered.fa 1 $genome.HelitronScanner.filtered.ext.fa.pass.fa -FA > $genome.HelitronScanner.filtered.fa.pass.fa`; +`${mdust}mdust $genome.HelitronScanner.filtered.fa.pass.fa > $genome.HelitronScanner.filtered.fa.pass.fa.dusted`; +`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 100 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.HelitronScanner.filtered.fa.pass.fa.dusted | perl -nle 's/^(>.*)\\s+(.*)\$/\$1#DNA\\/Helitron\\t\$2/; print \$_' > $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln`; + +# annotate and remove non-Helitron candidates +`${TEsorter}TEsorter $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; +`perl $cleanup_misclas $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.rexdb.cls.tsv`; +`mv $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln $genome.Helitron.intact.raw.fa`; +`cp $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln.list $genome.Helitron.intact.raw.fa.anno.list`; +`cp $genome.Helitron.intact.raw.fa.anno.list ../`; + +# get intact Helitrons and gff3 +`perl $make_bed $genome.Helitron.intact.raw.fa > $genome.Helitron.intact.raw.bed`; +`perl $bed2gff $genome.Helitron.intact.raw.bed HEL > $genome.Helitron.intact.raw.gff3`; + } + +# copy result files out +`cp $genome.Helitron.intact.bed ../$genome.Helitron.intact.raw.bed` if -s "$genome.Helitron.intact.bed"; # recover /dev/null`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: Helitron results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.Helitron.intact.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.Helitron.intact.raw.fa"){ + print STDERR "$date\tFinish finding Helitron candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The Helitron result file has 0 bp!\n\n"; + } + +} + +chomp ($date = `date`); +print STDERR "$date\tExecution of EDTA_raw.pl is finished!\n\n"; diff --git a/bin/setup_LTR_retriever_postprocess.sh b/bin/setup_LTR_retriever_postprocess.sh new file mode 100755 index 0000000..140b4b5 --- /dev/null +++ b/bin/setup_LTR_retriever_postprocess.sh @@ -0,0 +1,26 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/LTR_retriever_postprocess.pl << EOF + +my \$genome = 'genome'; +my \$threads = $1; + +my \$call_seq = '$script_path/call_seq_by_list.pl'; +my \$rename_LTR = '$script_path/rename_LTR_skim.pl'; +my \$mdust = ''; # Assumed on PATH +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; +my \$trf = '$(which trf)'; +my \$TEsorter = ''; # Assumed on PATH +my \$cleanup_misclas= '$script_path/cleanup_misclas.pl'; +my \$output_by_list = '$script_path/output_by_list.pl'; +my \$filter_gff = '$script_path/filter_gff3.pl'; + +EOF + +sed -n 443,462p "$script_path/EDTA_raw.pl" \ + >> input/LTR_retriever_postprocess.pl + +sed -n 466,472p "$script_path/EDTA_raw.pl" \ + >> input/LTR_retriever_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index 918b569..c521005 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -42,5 +42,15 @@ process { withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' } + + withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/ltr" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/conf/test.config b/conf/test.config index e921133..e0a2931 100644 --- a/conf/test.config +++ b/conf/test.config @@ -7,5 +7,5 @@ process { } params { - genomes = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' + genomes = 'https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa' } \ No newline at end of file diff --git a/modules/local/ltr_retriever_postprocess/environment.yml b/modules/local/ltr_retriever_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/ltr_retriever_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf new file mode 100644 index 0000000..c957229 --- /dev/null +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -0,0 +1,80 @@ +process LTR_RETRIEVER_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/genome.pass.list" + path "input/genome.pass.list.gff3" + path "input/genome.defalse" + path "input/genome.LTRlib.fa" + + output: + tuple val(meta), path('*.LTR.raw.fa') , emit: raw_fa + tuple val(meta), path('*.LTR.intact.raw.fa') , emit: intact_raw_fa + tuple val(meta), path('*.LTR.intact.raw.gff3') , emit: intact_raw_gff3 + tuple val(meta), path('*.LTR.intact.raw.fa.anno.list') , emit: anno_list + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_LTR_retriever_postprocess.sh \\ + $task.cpus + + cd input + + perl LTR_retriever_postprocess.pl + + cd - + + mv \\ + genome.LTR.raw.fa \\ + ${prefix}.LTR.raw.fa + + mv \\ + genome.LTR.intact.raw.fa \\ + ${prefix}.genome.LTR.intact.raw.fa + + mv \\ + genome.LTR.intact.raw.gff3 \\ + ${prefix}.LTR.intact.raw.gff3 + + mv \\ + genome.LTR.intact.raw.fa.anno.list \\ + ${prefix}.LTR.intact.raw.fa.anno.list + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/nf-core/ltrretriever/ltrretriever/main.nf b/modules/nf-core/ltrretriever/ltrretriever/main.nf index 8e1e2be..ca97232 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/main.nf +++ b/modules/nf-core/ltrretriever/ltrretriever/main.nf @@ -21,6 +21,7 @@ process LTRRETRIEVER_LTRRETRIEVER { tuple val(meta), path("*.LTRlib.fa") , emit: ltrlib , optional: true tuple val(meta), path("${prefix}.out") , emit: annotation_out , optional: true tuple val(meta), path("*.out.gff3") , emit: annotation_gff , optional: true + tuple val(meta), path("*.defalse") , emit: defalse , optional: true path "versions.yml" , emit: versions when: @@ -66,6 +67,7 @@ process LTRRETRIEVER_LTRRETRIEVER { mv "${writable_genome}.LTRlib.fa" "${prefix}.LTRlib.fa" || echo ".LTRlib.fa was not produced" mv "${writable_genome}.out" "${prefix}.out" || echo ".out was not produced" mv "${writable_genome}.out.gff3" "${prefix}.out.gff3" || echo ".out.gff3 was not produced" + mv "${writable_genome}.defalse" "${prefix}.defalse" || echo ".defalse was not produced" cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap index 825b1e5..4942e1a 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap @@ -61,6 +61,9 @@ ] ], "6": [ + + ], + "7": [ "versions.yml:md5,3ab159acaee06b342b56e2d35e5e669b" ], "annotation_gff": [ @@ -78,6 +81,9 @@ }, "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "defalse": [ + ], "log": [ [ @@ -117,10 +123,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-19T11:04:15.954424" + "timestamp": "2024-12-05T12:39:11.669541" }, "annotation_out": { "content": [ @@ -151,4 +157,4 @@ }, "timestamp": "2024-07-16T14:03:52.324194" } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index ccf5850..7eb1232 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,3 +1,7 @@ +params { + publish_dir_mode = 'copy' +} + process { cpus = { 1 * task.attempt } diff --git a/nf-test.config b/nf-test.config index c3a9a1e..29d7e09 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,7 +1,7 @@ config { testsDir "." workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" - configFile "test/nf-test/nextflow.config" + configFile "tests/nf-test/nextflow.config" plugins { load "nft-bam@0.4.0" diff --git a/test/Alyrata.test.fa b/tests/Alyrata.test.fa similarity index 100% rename from test/Alyrata.test.fa rename to tests/Alyrata.test.fa diff --git a/test/Col.test.fa b/tests/Col.test.fa similarity index 100% rename from test/Col.test.fa rename to tests/Col.test.fa diff --git a/test/Ler.test.fa b/tests/Ler.test.fa similarity index 100% rename from test/Ler.test.fa rename to tests/Ler.test.fa diff --git a/test/README.txt b/tests/README.txt similarity index 100% rename from test/README.txt rename to tests/README.txt diff --git a/test/genome.cds.fa b/tests/genome.cds.fa similarity index 100% rename from test/genome.cds.fa rename to tests/genome.cds.fa diff --git a/test/genome.cds.list b/tests/genome.cds.list similarity index 100% rename from test/genome.cds.list rename to tests/genome.cds.list diff --git a/test/genome.exclude.bed b/tests/genome.exclude.bed similarity index 100% rename from test/genome.exclude.bed rename to tests/genome.exclude.bed diff --git a/test/genome.fa b/tests/genome.fa similarity index 100% rename from test/genome.fa rename to tests/genome.fa diff --git a/test/nf-test/nextflow.config b/tests/nf-test/nextflow.config similarity index 100% rename from test/nf-test/nextflow.config rename to tests/nf-test/nextflow.config diff --git a/test/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test similarity index 50% rename from test/nf-test/small/main.nf.test rename to tests/nf-test/small/main.nf.test index 7d40a02..ce37a4f 100644 --- a/test/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -13,7 +13,28 @@ nextflow_pipeline { } then { - def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + def stable_path = getAllFilesFromDir( + params.outdir, + false, + [ + 'pipeline_info/*.{html,json,txt,yml}', + 'ltr/*.pp.LTR.intact.raw.gff3', + 'ltr/*.pp.LTR.raw.fa', + ], + null, + ['**'] + ) + + def stable_name = getAllFilesFromDir( + params.outdir, + true, + [ + 'pipeline_info/*.{html,json,txt,yml}' + ], + null, + ['**'] + ) assertAll( { assert workflow.success}, @@ -21,7 +42,8 @@ nextflow_pipeline { [ 'successful tasks': workflow.trace.succeeded().size(), 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), - 'stable paths': stable_path + 'stable paths': stable_path, + 'stable names': getRelativePath(stable_name, outputDir), ] ).match() } ) diff --git a/test/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap similarity index 72% rename from test/nf-test/small/main.nf.test.snap rename to tests/nf-test/small/main.nf.test.snap index 5a164b2..a943b0a 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 16, + "successful tasks": 17, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -42,6 +42,12 @@ "LTRRETRIEVER_LTRRETRIEVER": { "LTR_retriever": "v2.9.9" }, + "LTR_RETRIEVER_POSTPROCESS": { + "perl": "v5.32.1", + "trf": 4.09, + "TEsorter": "1.4.7", + "mdust": "2006.10.17" + }, "REPEATMODELER_BUILDDATABASE": { "repeatmodeler": "2.0.5" }, @@ -56,7 +62,16 @@ } }, "stable paths": [ - + "genome.pp.LTR.intact.raw.fa.anno.list:md5,51261f020350b448acdf89d8fb625448", + "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25" + ], + "stable names": [ + "ltr", + "ltr/genome.pp.LTR.intact.raw.fa.anno.list", + "ltr/genome.pp.LTR.intact.raw.gff3", + "ltr/genome.pp.LTR.raw.fa", + "ltr/genome.pp.genome.LTR.intact.raw.fa", + "pipeline_info" ] } ], @@ -64,6 +79,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-03T14:20:03.748125" + "timestamp": "2024-12-05T12:10:52.622584" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test b/tests/nf-test/tiny/main.nf.test similarity index 100% rename from test/nf-test/tiny/main.nf.test rename to tests/nf-test/tiny/main.nf.test diff --git a/test/nf-test/tiny/main.nf.test.snap b/tests/nf-test/tiny/main.nf.test.snap similarity index 100% rename from test/nf-test/tiny/main.nf.test.snap rename to tests/nf-test/tiny/main.nf.test.snap diff --git a/workflows/edta.nf b/workflows/edta.nf index 05a6da3..a4799cf 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -9,11 +9,14 @@ include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmod include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' +include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' workflow EDTA { + main: + // Versions channel ch_versions = Channel.empty() @@ -36,7 +39,6 @@ workflow EDTA { // MODULE: LTRHARVEST LTRHARVEST ( ch_sanitized_fasta ) - ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 ch_ltrharvest_scn = LTRHARVEST.out.scn ch_versions = ch_versions.mix(LTRHARVEST.out.versions) @@ -44,7 +46,6 @@ workflow EDTA { // MODULE: LTRFINDER LTRFINDER { ch_sanitized_fasta } - ch_ltrfinder_gff3 = LTRFINDER.out.gff ch_ltrfinder_scn = LTRFINDER.out.scn ch_versions = ch_versions.mix(LTRFINDER.out.versions) @@ -62,17 +63,17 @@ workflow EDTA { ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) LTRRETRIEVER_LTRRETRIEVER ( - ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, - ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, + ch_ltrretriever_inputs.map { meta, fasta, _ltr -> [ meta, fasta ] }, + ch_ltrretriever_inputs.map { _meta, _fasta, ltr -> ltr }, [], [], [] ) - ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list - ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out + ch_pass_list_gff = LTRRETRIEVER_LTRRETRIEVER.out.pass_list_gff ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff + ch_defalse = LTRRETRIEVER_LTRRETRIEVER.out.defalse ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) @@ -102,7 +103,7 @@ workflow EDTA { def size = fasta.size() def size_threshold = 100_000 // bytes -> bp - // TODO: Not the best way to set a size threshould + // TODO: Not the best way to set a size threshold // but it is simple // This is needed to avoid, // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. @@ -151,6 +152,32 @@ workflow EDTA { ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) + // MODULE: LTR_RETRIEVER_POSTPROCESS + ltr_retriever_postprocess_inputs = ch_sanitized_fasta + | join(ch_pass_list) + | join(ch_pass_list_gff) + | join(ch_annotation_gff) + | join(ch_defalse) + | join(ch_ltrlib) + | multiMap { meta, fasta, pass, p_gff, a_gff, defalse, ltr -> + genome: [ meta, fasta ] + pass : pass + p_gff : p_gff + a_gff : a_gff + defalse : defalse + ltr : ltr + } + + LTR_RETRIEVER_POSTPROCESS ( + ltr_retriever_postprocess_inputs.genome, + ltr_retriever_postprocess_inputs.pass, + ltr_retriever_postprocess_inputs.p_gff, + ltr_retriever_postprocess_inputs.defalse, + ltr_retriever_postprocess_inputs.ltr, + ) + + ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) + // Function: Save versions ch_versions = ch_versions @@ -168,4 +195,7 @@ workflow EDTA { cache: false ) + emit: + versions_yml = ch_versions_yml // [ software_versions.yml ] + } \ No newline at end of file From 427f3db1677fad77b0f0ffc9a3c1c9cd7b366a8b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 15:52:06 +1300 Subject: [PATCH 15/49] Fixed singularity container --- modules/local/ltr_retriever_postprocess/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf index c957229..e679be6 100644 --- a/modules/local/ltr_retriever_postprocess/main.nf +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -4,7 +4,7 @@ process LTR_RETRIEVER_POSTPROCESS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" input: From f68a619e98b05e34eb81b36312cd7195f9a37fa5 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 16:22:50 +1300 Subject: [PATCH 16/49] Fixed nextflow-setup version --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 20d4b62..d53140c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -56,7 +56,7 @@ jobs: uses: actions/checkout@v4.2.1 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@v2.0.0 with: version: "${{ matrix.NXF_VER }}" From f0491de3b57d4bf78dda24fe5af8e347c8255c1c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 13:23:12 +1300 Subject: [PATCH 17/49] Multiple changes --- .github/include.yaml | 10 ++ .github/workflows/ci.yml | 115 ++++++++++++-------- .gitignore | 2 + cleanNXF.sh | 15 +++ conf/test.config | 11 ++ main.nf | 162 ++++++++++++++++++++++++++++ modules/local/utils/main.nf | 44 ++++++++ nextflow.config | 99 +++++++++++++++++ nf-test.config | 10 ++ test/nf-test/nextflow.config | 22 ++++ test/nf-test/tiny/main.nf.test | 32 ++++++ test/nf-test/tiny/main.nf.test.snap | 42 ++++++++ 12 files changed, 517 insertions(+), 47 deletions(-) create mode 100644 .github/include.yaml create mode 100755 cleanNXF.sh create mode 100644 conf/test.config create mode 100755 main.nf create mode 100644 modules/local/utils/main.nf create mode 100644 nextflow.config create mode 100644 nf-test.config create mode 100644 test/nf-test/nextflow.config create mode 100644 test/nf-test/tiny/main.nf.test create mode 100644 test/nf-test/tiny/main.nf.test.snap diff --git a/.github/include.yaml b/.github/include.yaml new file mode 100644 index 0000000..5d850e1 --- /dev/null +++ b/.github/include.yaml @@ -0,0 +1,10 @@ +".": + - ./.github/workflows/** + - ./nf-test.config +tests: + - ./assets/* + - ./bin/* + - ./conf/* + - ./main.nf + - ./nextflow_schema.json + - ./nextflow.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6c27abd..43d4c6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,78 +1,99 @@ name: EDTA Nextflow CI on: - push: - branches: - - nextflow_reboot pull_request: - branches: - - nextflow_reboot env: NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + NFT_WORKDIR: "~" + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true - jobs: + nf-test-changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + nf_test_files: ${{ steps.list.outputs.components }} + steps: + - uses: actions/checkout@v4.2.1 + with: + fetch-depth: 0 + + - name: List nf-test files + id: list + uses: adamrtalbot/detect-nf-test-changes@v0.0.4 + with: + head: ${{ github.sha }} + base: origin/${{ github.base_ref }} + include: .github/include.yaml + + - name: print list of nf-test files + run: | + echo ${{ steps.list.outputs.components }} + test: - name: Run pipeline with test data - # Only run on push if this is the jguhlin nextflow_reboot branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'jguhlin/EDTA') }}" + name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} + needs: [nf-test-changes] + if: needs.nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - nextflow: - - '24.04.4' + NXF_VER: + - "24.04.2" + + nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - docker - - singularity - - conda + - "docker" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@v4.2.1 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 with: - version: ${{ matrix.nextflow }} + version: "${{ matrix.NXF_VER }}" - # - name: Disk space cleanup - # uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - # Will be needed with large data sets. Can take long to run + - uses: actions/setup-python@v5.2.0 + with: + python-version: "3.11" + architecture: "x64" - - name: Setup apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' + - name: Install pdiff to see diff between nf-test snapshots run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + python -m pip install --upgrade pip + pip install pdiff + + - uses: nf-core/setup-nf-test@v1.1.2 with: - miniconda-version: "latest" - auto-update-conda: true - channels: conda-forge,bioconda + version: 0.9.0 - - name: Conda setup - if: matrix.profile == 'conda' + - name: Disk space cleanup + if: matrix.nf_test_files == 'tests/stub/main.nf.test' + uses: jlumbroso/free-disk-space@v1.3.1 + + - name: Run nf-test run: | - conda clean -a - conda install -n base conda-libmamba-solver - conda config --set solver libmamba - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH + nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" + + confirm-pass: + runs-on: ubuntu-latest + needs: [test] + if: always() + steps: + - name: All tests ok + if: ${{ !contains(needs.*.result, 'failure') }} + run: exit 0 + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 - - name: Run pipeline with test data + - name: debug-print + if: always() run: | - nextflow run \ - ${GITHUB_WORKSPACE} \ - -profile ${{ matrix.profile }},test + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/.gitignore b/.gitignore index 9b1e821..f636970 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,5 @@ bin/TIR-Learner*/Module3/Maize_model.sav work/ .nextflow.log* .nextflow/* +results/ +.nf-test* diff --git a/cleanNXF.sh b/cleanNXF.sh new file mode 100755 index 0000000..81b8d85 --- /dev/null +++ b/cleanNXF.sh @@ -0,0 +1,15 @@ +#!/usr/bin/env bash + +rm -rf .nextflow* +echo "Cleaned .nextflow..." +rm -rf .nextflow.pid +echo "Cleaned .nextflow.pid..." +for i in $(ls work | grep -v "conda"); +do + rm -rf "work/$i" +done +echo "Cleaned work..." + +rm -f .nf-test.log +rm -rf .nf-test +echo "Cleaned nf-test..." diff --git a/conf/test.config b/conf/test.config new file mode 100644 index 0000000..e921133 --- /dev/null +++ b/conf/test.config @@ -0,0 +1,11 @@ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + genomes = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' +} \ No newline at end of file diff --git a/main.nf b/main.nf new file mode 100755 index 0000000..d49f489 --- /dev/null +++ b/main.nf @@ -0,0 +1,162 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +params.genomes = 'genomes/*' +params.species = 'others' +params.cds = '' +params.curatedlib = '' +params.rmlib = '' +params.sensitive = false +params.anno = false +params.rmout = '' +params.maxdiv = 40 +params.evaluate = true +params.exclude = '' +params.maxint = 5000 +params.outdir = 'results' + +// TODO: Check inputed repeat libraries, CDS, etc... +// TODO: Check exclude file + +include { SANITIZE_HEADERS } from './modules/local/sanitize/main.nf' +include { LTRHARVEST } from './modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from './modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from './modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from './modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { TIRLEARNER } from './modules/gallvp/tirlearner/main.nf' +include { ANNOSINE } from './modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from './modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from './modules/nf-core/repeatmodeler/repeatmodeler/main.nf' + +include { softwareVersionsToYAML } from './modules/local/utils/main.nf' + +// Test run: +// ./main.nf -profile docker,test +// ./main.nf -profile conda,test +workflow { + + // Versions channel + ch_versions = Channel.empty() + + + ch_genome = Channel.fromPath(params.genomes) + + // Create a meta object for each genome + ch_meta_genome = ch_genome.map { genome -> + def meta = [:] + meta.id = genome.baseName + + [ meta, genome ] + } + + // MODULE: SANITIZE_HEADERS + SANITIZE_HEADERS ( ch_meta_genome ) + + ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta + + // MODULE: LTRHARVEST + LTRHARVEST ( ch_sanitized_fasta ) + + ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 + ch_ltrharvest_scn = LTRHARVEST.out.scn + + ch_versions = ch_versions.mix(LTRHARVEST.out.versions) + + // MODULE: LTRFINDER + LTRFINDER { ch_sanitized_fasta } + + ch_ltrfinder_gff3 = LTRFINDER.out.gff + ch_ltrfinder_scn = LTRFINDER.out.scn + + ch_versions = ch_versions.mix(LTRFINDER.out.versions) + + // MODULE: CAT_CAT + ch_cat_cat_inputs = ch_ltrharvest_scn + | join(ch_ltrfinder_scn) + | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } + CAT_CAT ( ch_cat_cat_inputs ) + + ch_ltr_candidates = CAT_CAT.out.file_out + ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) + + // MODULE: LTRRETRIEVER_LTRRETRIEVER + ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) + + LTRRETRIEVER_LTRRETRIEVER ( + ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, + ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, + [], + [], + [] + ) + + ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log + ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list + ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out + ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff + ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib + ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) + + // MODULE: TIRLEARNER + TIRLEARNER ( + ch_sanitized_fasta, + params.species + ) + + ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff + ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + + // These can also run in parallel + // MODULE: ANNOSINE + ANNOSINE ( + ch_sanitized_fasta, + 3 // mode + ) + + // Currently it's a topic, so need to fix that + ch_versions = ch_versions.mix(ANNOSINE.out.versions) + cb_annosine_seed_sine = ANNOSINE.out.fa + + // MODULE: REPEATMODELER_BUILDDATABASE + ch_repeatmodeler_inputs = ch_sanitized_fasta + | map { meta, fasta -> + def size = fasta.size() + def size_threshold = 100_000 // bytes -> bp + + // TODO: Not the best way to set a size threshould + // but it is simple + // This is needed to avoid, + // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. + if ( size < size_threshold ) { + log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" + return null + } + + return [ meta, fasta ] + } + | filter { it } + + REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) + + ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db + ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) + + // MODULE: REPEATMODELER_REPEATMODELER + REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) + + ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta + ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + + + // Function: Save versions + ch_versions_yml = softwareVersionsToYAML(ch_versions) + | collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'software_versions.yml', + sort: true, + newLine: true, + cache: false + ) + +} diff --git a/modules/local/utils/main.nf b/modules/local/utils/main.nf new file mode 100644 index 0000000..fee91f3 --- /dev/null +++ b/modules/local/utils/main.nf @@ -0,0 +1,44 @@ +// +// Generate workflow version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000..12a89b6 --- /dev/null +++ b/nextflow.config @@ -0,0 +1,99 @@ +process { + + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + maxRetries = 1 + maxErrors = '-1' + + withLabel:process_single { + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + } + withLabel:process_low { + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } + } + withLabel:process_medium { + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } + } + withLabel:process_high { + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } + } + withLabel:process_long { + time = { 20.h * task.attempt } + } + withLabel:process_high_memory { + memory = { 200.GB * task.attempt } + } + withLabel:error_ignore { + errorStrategy = 'ignore' + } + withLabel:error_retry { + errorStrategy = 'retry' + maxRetries = 2 + } +} + +// Max resources +process { + resourceLimits = [ + cpus: 12, + memory: '16.GB', + time: '1.hour' + ] +} + +profiles { + singularity { + singularity.enabled = true + singularity.autoMounts = true + } + apptainer { + apptainer.enabled = true + apptainer.autoMounts = true + } + conda { + conda.enabled = true + } + mamba { + conda.enabled = true + conda.useMamba = true + } + podman { + podman.enabled = true + podman.userEmulation = true + podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" + } + docker { + docker.enabled = true + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } + test { includeConfig './conf/test.config' } +} + +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +apptainer.registry = 'quay.io' + +// Increase time available to build Conda environment +conda { + createTimeout = "120 min" +} + +manifest { + name = 'jguhlin/EDTA' + nextflowVersion = '!>=23.04.0' + version = '0.1.0dev' +} + +includeConfig 'conf/modules.config' diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 0000000..c3a9a1e --- /dev/null +++ b/nf-test.config @@ -0,0 +1,10 @@ +config { + testsDir "." + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + configFile "test/nf-test/nextflow.config" + + plugins { + load "nft-bam@0.4.0" + load "nft-utils@0.0.3" + } +} diff --git a/test/nf-test/nextflow.config b/test/nf-test/nextflow.config new file mode 100644 index 0000000..ed1a805 --- /dev/null +++ b/test/nf-test/nextflow.config @@ -0,0 +1,22 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +} + +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} diff --git a/test/nf-test/tiny/main.nf.test b/test/nf-test/tiny/main.nf.test new file mode 100644 index 0000000..5022c49 --- /dev/null +++ b/test/nf-test/tiny/main.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test with a tiny genome" + script "main.nf" + + test("tiny genome") { + + when { + params { + genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + outdir = "$outputDir" + } + } + + then { + def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + assertAll( + { assert workflow.success}, + { assert snapshot( + [ + 'successful tasks': workflow.trace.succeeded().size(), + 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), + 'stable paths': stable_path + ] + ).match() } + ) + } + + } + +} diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap new file mode 100644 index 0000000..a61631f --- /dev/null +++ b/test/nf-test/tiny/main.nf.test.snap @@ -0,0 +1,42 @@ +{ + "tiny genome": { + "content": [ + { + "successful tasks": 7, + "versions": { + "ANNOSINE": { + "annosine": "2.0.7" + }, + "CAT_CAT": { + "pigz": "2.3.4" + }, + "LTRFINDER": { + "LTR_FINDER_parallel": "v1.1", + "ltr_finder": "v1.07" + }, + "LTRHARVEST": { + "LTR_HARVEST_parallel": "v1.1", + "genometools": "1.6.5" + }, + "LTRRETRIEVER_LTRRETRIEVER": { + "LTR_retriever": "v2.9.9" + }, + "TIRLEARNER": { + "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + }, + "Workflow": { + "jguhlin/EDTA": "v0.1.0dev" + } + }, + "stable paths": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-25T13:20:57.770583" + } +} \ No newline at end of file From 74edd95010e66055c9c81f1a4ca398050344c0d4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 14:44:00 +1300 Subject: [PATCH 18/49] Updated test CI --- main.nf | 6 ++++ test/nf-test/small/main.nf.test | 32 +++++++++++++++++++ test/nf-test/small/main.nf.test.snap | 48 ++++++++++++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 test/nf-test/small/main.nf.test create mode 100644 test/nf-test/small/main.nf.test.snap diff --git a/main.nf b/main.nf index d49f489..091684c 100755 --- a/main.nf +++ b/main.nf @@ -150,6 +150,12 @@ workflow { // Function: Save versions + ch_versions = ch_versions + | unique + | map { yml -> + if ( yml ) { yml } + } + ch_versions_yml = softwareVersionsToYAML(ch_versions) | collectFile( storeDir: "${params.outdir}/pipeline_info", diff --git a/test/nf-test/small/main.nf.test b/test/nf-test/small/main.nf.test new file mode 100644 index 0000000..4cb9c26 --- /dev/null +++ b/test/nf-test/small/main.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test with a small genome" + script "main.nf" + + test("small genome") { + + when { + params { + genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" + outdir = "$outputDir" + } + } + + then { + def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + assertAll( + { assert workflow.success}, + { assert snapshot( + [ + 'successful tasks': workflow.trace.succeeded().size(), + 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), + 'stable paths': stable_path + ] + ).match() } + ) + } + + } + +} diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap new file mode 100644 index 0000000..d53e834 --- /dev/null +++ b/test/nf-test/small/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "small genome": { + "content": [ + { + "successful tasks": 9, + "versions": { + "ANNOSINE": { + "annosine": "2.0.7" + }, + "CAT_CAT": { + "pigz": "2.3.4" + }, + "LTRFINDER": { + "LTR_FINDER_parallel": "v1.1", + "ltr_finder": "v1.07" + }, + "LTRHARVEST": { + "LTR_HARVEST_parallel": "v1.1", + "genometools": "1.6.5" + }, + "LTRRETRIEVER_LTRRETRIEVER": { + "LTR_retriever": "v2.9.9" + }, + "REPEATMODELER_BUILDDATABASE": { + "repeatmodeler": "2.0.5" + }, + "REPEATMODELER_REPEATMODELER": { + "repeatmodeler": "2.0.5" + }, + "TIRLEARNER": { + "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + }, + "Workflow": { + "jguhlin/EDTA": "v0.1.0dev" + } + }, + "stable paths": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-25T13:53:22.07666" + } +} \ No newline at end of file From cbd0d2f431d814aa5b95e144d6b519206fcc512c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 15:23:50 +1300 Subject: [PATCH 19/49] Added missing modules, profiles and manifest fields --- .github/workflows/ci.yml | 18 ++- conf/modules.config | 23 +++ main.nf | 147 +----------------- modules.json | 68 ++++++++ modules/gallvp/gunzip/environment.yml | 7 + modules/gallvp/gunzip/main.nf | 55 +++++++ modules/gallvp/gunzip/meta.yml | 47 ++++++ modules/gallvp/gunzip/tests/main.nf.test | 121 ++++++++++++++ modules/gallvp/gunzip/tests/main.nf.test.snap | 134 ++++++++++++++++ modules/gallvp/gunzip/tests/nextflow.config | 5 + modules/gallvp/gunzip/tests/tags.yml | 2 + modules/nf-core/gunzip/environment.yml | 7 + modules/nf-core/gunzip/main.nf | 55 +++++++ modules/nf-core/gunzip/meta.yml | 47 ++++++ modules/nf-core/gunzip/tests/main.nf.test | 121 ++++++++++++++ .../nf-core/gunzip/tests/main.nf.test.snap | 134 ++++++++++++++++ modules/nf-core/gunzip/tests/nextflow.config | 5 + modules/nf-core/gunzip/tests/tags.yml | 2 + nextflow.config | 4 +- workflows/edta.nf | 144 +++++++++++++++++ 20 files changed, 996 insertions(+), 150 deletions(-) create mode 100644 conf/modules.config create mode 100644 modules.json create mode 100644 modules/gallvp/gunzip/environment.yml create mode 100644 modules/gallvp/gunzip/main.nf create mode 100644 modules/gallvp/gunzip/meta.yml create mode 100644 modules/gallvp/gunzip/tests/main.nf.test create mode 100644 modules/gallvp/gunzip/tests/main.nf.test.snap create mode 100644 modules/gallvp/gunzip/tests/nextflow.config create mode 100644 modules/gallvp/gunzip/tests/tags.yml create mode 100644 modules/nf-core/gunzip/environment.yml create mode 100644 modules/nf-core/gunzip/main.nf create mode 100644 modules/nf-core/gunzip/meta.yml create mode 100644 modules/nf-core/gunzip/tests/main.nf.test create mode 100644 modules/nf-core/gunzip/tests/main.nf.test.snap create mode 100644 modules/nf-core/gunzip/tests/nextflow.config create mode 100644 modules/nf-core/gunzip/tests/tags.yml create mode 100644 workflows/edta.nf diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 43d4c6c..20d4b62 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,10 +7,13 @@ env: NFT_WORKDIR: "~" NFT_DIFF: "pdiff" NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true + jobs: nf-test-changes: name: Check for changes @@ -46,8 +49,7 @@ jobs: - "24.04.2" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] - profile: - - "docker" + profile: [conda, docker, singularity] steps: - name: Check out pipeline code @@ -71,10 +73,16 @@ jobs: - uses: nf-core/setup-nf-test@v1.1.2 with: version: 0.9.0 + + - name: Setup apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Disk space cleanup - if: matrix.nf_test_files == 'tests/stub/main.nf.test' - uses: jlumbroso/free-disk-space@v1.3.1 + - name: Set up Singularity + if: matrix.profile == 'singularity' + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR - name: Run nf-test run: | diff --git a/conf/modules.config b/conf/modules.config new file mode 100644 index 0000000..81d11dc --- /dev/null +++ b/conf/modules.config @@ -0,0 +1,23 @@ +process { + withName: 'EDTA:LTRHARVEST' { + ext.args = '-size 1000000 -time 300' + ext.prefix = { "${meta.id}_ltrharvest" } + } + + withName: 'EDTA:LTRFINDER' { + ext.args = '-harvest_out -size 1000000 -time 300' + } + + withName: 'EDTA:CAT_CAT' { + ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } + } + + withName: 'EDTA:ANNOSINE' { + ext.args = '--num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' + } + + withName: 'EDTA:REPEATMODELER_REPEATMODELER' { + ext.args = '-engine ncbi' + } + +} \ No newline at end of file diff --git a/main.nf b/main.nf index 091684c..fa74a8b 100755 --- a/main.nf +++ b/main.nf @@ -16,153 +16,12 @@ params.exclude = '' params.maxint = 5000 params.outdir = 'results' -// TODO: Check inputed repeat libraries, CDS, etc... -// TODO: Check exclude file - -include { SANITIZE_HEADERS } from './modules/local/sanitize/main.nf' -include { LTRHARVEST } from './modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from './modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from './modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from './modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { TIRLEARNER } from './modules/gallvp/tirlearner/main.nf' -include { ANNOSINE } from './modules/gallvp/annosine/main.nf' -include { REPEATMODELER_BUILDDATABASE } from './modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from './modules/nf-core/repeatmodeler/repeatmodeler/main.nf' - -include { softwareVersionsToYAML } from './modules/local/utils/main.nf' +include { EDTA } from './workflows/edta.nf' // Test run: // ./main.nf -profile docker,test // ./main.nf -profile conda,test -workflow { - - // Versions channel - ch_versions = Channel.empty() - - - ch_genome = Channel.fromPath(params.genomes) - - // Create a meta object for each genome - ch_meta_genome = ch_genome.map { genome -> - def meta = [:] - meta.id = genome.baseName - - [ meta, genome ] - } - - // MODULE: SANITIZE_HEADERS - SANITIZE_HEADERS ( ch_meta_genome ) - - ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta - - // MODULE: LTRHARVEST - LTRHARVEST ( ch_sanitized_fasta ) - - ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 - ch_ltrharvest_scn = LTRHARVEST.out.scn - - ch_versions = ch_versions.mix(LTRHARVEST.out.versions) - - // MODULE: LTRFINDER - LTRFINDER { ch_sanitized_fasta } - - ch_ltrfinder_gff3 = LTRFINDER.out.gff - ch_ltrfinder_scn = LTRFINDER.out.scn - - ch_versions = ch_versions.mix(LTRFINDER.out.versions) - - // MODULE: CAT_CAT - ch_cat_cat_inputs = ch_ltrharvest_scn - | join(ch_ltrfinder_scn) - | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } - CAT_CAT ( ch_cat_cat_inputs ) - - ch_ltr_candidates = CAT_CAT.out.file_out - ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) - - // MODULE: LTRRETRIEVER_LTRRETRIEVER - ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) - - LTRRETRIEVER_LTRRETRIEVER ( - ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, - ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, - [], - [], - [] - ) - - ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log - ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list - ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out - ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff - ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib - ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) - - // MODULE: TIRLEARNER - TIRLEARNER ( - ch_sanitized_fasta, - params.species - ) - - ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff - ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) - - // These can also run in parallel - // MODULE: ANNOSINE - ANNOSINE ( - ch_sanitized_fasta, - 3 // mode - ) - - // Currently it's a topic, so need to fix that - ch_versions = ch_versions.mix(ANNOSINE.out.versions) - cb_annosine_seed_sine = ANNOSINE.out.fa - - // MODULE: REPEATMODELER_BUILDDATABASE - ch_repeatmodeler_inputs = ch_sanitized_fasta - | map { meta, fasta -> - def size = fasta.size() - def size_threshold = 100_000 // bytes -> bp - - // TODO: Not the best way to set a size threshould - // but it is simple - // This is needed to avoid, - // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. - if ( size < size_threshold ) { - log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" - return null - } - - return [ meta, fasta ] - } - | filter { it } - - REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) - - ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db - ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) - - // MODULE: REPEATMODELER_REPEATMODELER - REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) - - ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta - ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) - - - // Function: Save versions - ch_versions = ch_versions - | unique - | map { yml -> - if ( yml ) { yml } - } - - ch_versions_yml = softwareVersionsToYAML(ch_versions) - | collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'software_versions.yml', - sort: true, - newLine: true, - cache: false - ) +workflow { + EDTA() } diff --git a/modules.json b/modules.json new file mode 100644 index 0000000..f9eedd5 --- /dev/null +++ b/modules.json @@ -0,0 +1,68 @@ +{ + "name": "", + "homePage": "", + "repos": { + "https://github.com/GallVp/nxf-components.git": { + "modules": { + "gallvp": { + "annosine": { + "branch": "main", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", + "installed_by": ["modules"] + }, + "gunzip": { + "branch": "main", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", + "installed_by": ["modules"] + }, + "tirlearner": { + "branch": "main", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", + "installed_by": ["modules"] + } + } + } + }, + "https://github.com/nf-core/modules.git": { + "modules": { + "nf-core": { + "cat/cat": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "gunzip": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "ltrfinder": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "ltrharvest": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "ltrretriever/ltrretriever": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "repeatmodeler/builddatabase": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, + "repeatmodeler/repeatmodeler": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + } + } + } + } + } +} diff --git a/modules/gallvp/gunzip/environment.yml b/modules/gallvp/gunzip/environment.yml new file mode 100644 index 0000000..c779485 --- /dev/null +++ b/modules/gallvp/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/gallvp/gunzip/main.nf b/modules/gallvp/gunzip/main.nf new file mode 100644 index 0000000..5e67e3b --- /dev/null +++ b/modules/gallvp/gunzip/main.nf @@ -0,0 +1,55 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ + $args \\ + $archive \\ + > $gunzip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/gallvp/gunzip/meta.yml b/modules/gallvp/gunzip/meta.yml new file mode 100644 index 0000000..9066c03 --- /dev/null +++ b/modules/gallvp/gunzip/meta.yml @@ -0,0 +1,47 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/gallvp/gunzip/tests/main.nf.test b/modules/gallvp/gunzip/tests/main.nf.test new file mode 100644 index 0000000..f661057 --- /dev/null +++ b/modules/gallvp/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_gallvp" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/gunzip/tests/main.nf.test.snap b/modules/gallvp/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..069967e --- /dev/null +++ b/modules/gallvp/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/gallvp/gunzip/tests/nextflow.config b/modules/gallvp/gunzip/tests/nextflow.config new file mode 100644 index 0000000..dec7764 --- /dev/null +++ b/modules/gallvp/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/gallvp/gunzip/tests/tags.yml b/modules/gallvp/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/gallvp/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 0000000..c779485 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf new file mode 100644 index 0000000..5e67e3b --- /dev/null +++ b/modules/nf-core/gunzip/main.nf @@ -0,0 +1,55 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ + $args \\ + $archive \\ + > $gunzip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml new file mode 100644 index 0000000..9066c03 --- /dev/null +++ b/modules/nf-core/gunzip/meta.yml @@ -0,0 +1,47 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 0000000..776211a --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 0000000..069967e --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 0000000..dec7764 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 0000000..fd3f691 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/nextflow.config b/nextflow.config index 12a89b6..34dfae1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -92,8 +92,10 @@ conda { manifest { name = 'jguhlin/EDTA' - nextflowVersion = '!>=23.04.0' + description = 'Extensive de-novo TE Annotator on Nextflow' + manifest.author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' version = '0.1.0dev' + nextflowVersion = '!>=23.04.0' } includeConfig 'conf/modules.config' diff --git a/workflows/edta.nf b/workflows/edta.nf new file mode 100644 index 0000000..df8b2d9 --- /dev/null +++ b/workflows/edta.nf @@ -0,0 +1,144 @@ +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' +include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' + +include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' + +workflow EDTA { + + // Versions channel + ch_versions = Channel.empty() + + + ch_genome = Channel.fromPath(params.genomes) + + // Create a meta object for each genome + ch_meta_genome = ch_genome.map { genome -> + def meta = [:] + meta.id = genome.baseName + + [ meta, genome ] + } + + // MODULE: SANITIZE_HEADERS + SANITIZE_HEADERS ( ch_meta_genome ) + + ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta + + // MODULE: LTRHARVEST + LTRHARVEST ( ch_sanitized_fasta ) + + ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 + ch_ltrharvest_scn = LTRHARVEST.out.scn + + ch_versions = ch_versions.mix(LTRHARVEST.out.versions) + + // MODULE: LTRFINDER + LTRFINDER { ch_sanitized_fasta } + + ch_ltrfinder_gff3 = LTRFINDER.out.gff + ch_ltrfinder_scn = LTRFINDER.out.scn + + ch_versions = ch_versions.mix(LTRFINDER.out.versions) + + // MODULE: CAT_CAT + ch_cat_cat_inputs = ch_ltrharvest_scn + | join(ch_ltrfinder_scn) + | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } + CAT_CAT ( ch_cat_cat_inputs ) + + ch_ltr_candidates = CAT_CAT.out.file_out + ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) + + // MODULE: LTRRETRIEVER_LTRRETRIEVER + ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) + + LTRRETRIEVER_LTRRETRIEVER ( + ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, + ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, + [], + [], + [] + ) + + ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log + ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list + ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out + ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff + ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib + ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) + + // MODULE: TIRLEARNER + TIRLEARNER ( + ch_sanitized_fasta, + params.species + ) + + ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff + ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + + // These can also run in parallel + // MODULE: ANNOSINE + ANNOSINE ( + ch_sanitized_fasta, + 3 // mode + ) + + // Currently it's a topic, so need to fix that + ch_versions = ch_versions.mix(ANNOSINE.out.versions) + cb_annosine_seed_sine = ANNOSINE.out.fa + + // MODULE: REPEATMODELER_BUILDDATABASE + ch_repeatmodeler_inputs = ch_sanitized_fasta + | map { meta, fasta -> + def size = fasta.size() + def size_threshold = 100_000 // bytes -> bp + + // TODO: Not the best way to set a size threshould + // but it is simple + // This is needed to avoid, + // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. + if ( size < size_threshold ) { + log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" + return null + } + + return [ meta, fasta ] + } + | filter { it } + + REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) + + ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db + ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) + + // MODULE: REPEATMODELER_REPEATMODELER + REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) + + ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta + ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + + + // Function: Save versions + ch_versions = ch_versions + | unique + | map { yml -> + if ( yml ) { yml } + } + + ch_versions_yml = softwareVersionsToYAML(ch_versions) + | collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'software_versions.yml', + sort: true, + newLine: true, + cache: false + ) + +} \ No newline at end of file From b55514543dd690f4d1e5070526f723886ed10dea Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 25 Nov 2024 15:41:03 +1300 Subject: [PATCH 20/49] Now using EDTA's test genome for the small test --- test/nf-test/small/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/nf-test/small/main.nf.test b/test/nf-test/small/main.nf.test index 4cb9c26..7d40a02 100644 --- a/test/nf-test/small/main.nf.test +++ b/test/nf-test/small/main.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { when { params { - genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz" + genomes = "https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa" outdir = "$outputDir" } } From bdfe5ffe82fd105d45fafc92713aaeb79984a7be Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 21:42:17 +1300 Subject: [PATCH 21/49] Updated PR template --- .github/PULL_REQUEST_TEMPLATE.md | 11 +++++------ nextflow.config | 2 +- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index a78bd61..7919df0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,19 +1,18 @@ ## PR checklist -- [ ] PR to `nextflow_reboot` branch -- [ ] `conda` and `container` directives. -- [ ] Docker container + singularity container (optional) +For Nextflow implementation, + +- [ ] `conda` and `container` directives are included for each process +- [ ] Docker container + singularity container (optional) are included for each process - [ ] Flow `meta.id` with each data channel - [ ] Use nf-core resource labels such as `process_high` - [ ] Used nf-core module diff --git a/nextflow.config b/nextflow.config index 34dfae1..ccf5850 100644 --- a/nextflow.config +++ b/nextflow.config @@ -93,7 +93,7 @@ conda { manifest { name = 'jguhlin/EDTA' description = 'Extensive de-novo TE Annotator on Nextflow' - manifest.author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' + author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' version = '0.1.0dev' nextflowVersion = '!>=23.04.0' } From aaae5e88dbce8046c55bdc94669817474a10fd43 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 22:21:39 +1300 Subject: [PATCH 22/49] Added fasta_helitronscanner_scan_draw --- conf/modules.config | 19 +++ modules.json | 19 +++ .../helitronscanner/draw/environment.yml | 7 + modules/gallvp/helitronscanner/draw/main.nf | 73 ++++++++ modules/gallvp/helitronscanner/draw/meta.yml | 69 ++++++++ .../helitronscanner/draw/tests/main.nf.test | 159 ++++++++++++++++++ .../draw/tests/main.nf.test.snap | 80 +++++++++ .../draw/tests/nextflow.config | 5 + .../helitronscanner/scan/environment.yml | 5 + modules/gallvp/helitronscanner/scan/main.nf | 72 ++++++++ modules/gallvp/helitronscanner/scan/meta.yml | 60 +++++++ .../helitronscanner/scan/tests/main.nf.test | 148 ++++++++++++++++ .../scan/tests/main.nf.test.snap | 104 ++++++++++++ .../fasta_helitronscanner_scan_draw/main.nf | 86 ++++++++++ .../fasta_helitronscanner_scan_draw/meta.yml | 45 +++++ .../tests/main.nf.test | 97 +++++++++++ .../tests/main.nf.test.snap | 137 +++++++++++++++ .../tests/nextflow.config | 20 +++ workflows/edta.nf | 26 +-- 19 files changed, 1220 insertions(+), 11 deletions(-) create mode 100644 modules/gallvp/helitronscanner/draw/environment.yml create mode 100644 modules/gallvp/helitronscanner/draw/main.nf create mode 100644 modules/gallvp/helitronscanner/draw/meta.yml create mode 100644 modules/gallvp/helitronscanner/draw/tests/main.nf.test create mode 100644 modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap create mode 100644 modules/gallvp/helitronscanner/draw/tests/nextflow.config create mode 100644 modules/gallvp/helitronscanner/scan/environment.yml create mode 100644 modules/gallvp/helitronscanner/scan/main.nf create mode 100644 modules/gallvp/helitronscanner/scan/meta.yml create mode 100644 modules/gallvp/helitronscanner/scan/tests/main.nf.test create mode 100644 modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap create mode 100644 subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config diff --git a/conf/modules.config b/conf/modules.config index 81d11dc..e70a6ea 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -19,5 +19,24 @@ process { withName: 'EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '-pure_helitron' + } } \ No newline at end of file diff --git a/modules.json b/modules.json index f9eedd5..5d34d4e 100644 --- a/modules.json +++ b/modules.json @@ -15,12 +15,31 @@ "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["modules"] }, + "helitronscanner/draw": { + "branch": "main", + "git_sha": "929d59d82f2e90fe79eb6f93d1ae739f22a894e1", + "installed_by": ["fasta_helitronscanner_scan_draw"] + }, + "helitronscanner/scan": { + "branch": "main", + "git_sha": "929d59d82f2e90fe79eb6f93d1ae739f22a894e1", + "installed_by": ["fasta_helitronscanner_scan_draw"] + }, "tirlearner": { "branch": "main", "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] } } + }, + "subworkflows": { + "gallvp": { + "fasta_helitronscanner_scan_draw": { + "branch": "main", + "git_sha": "970e3af38229845dd38c13d29b0905651a8e61f0", + "installed_by": ["subworkflows"] + } + } } }, "https://github.com/nf-core/modules.git": { diff --git a/modules/gallvp/helitronscanner/draw/environment.yml b/modules/gallvp/helitronscanner/draw/environment.yml new file mode 100644 index 0000000..479f61c --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::helitronscanner=1.0" diff --git a/modules/gallvp/helitronscanner/draw/main.nf b/modules/gallvp/helitronscanner/draw/main.nf new file mode 100644 index 0000000..16ee59a --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/main.nf @@ -0,0 +1,73 @@ +process HELITRONSCANNER_DRAW { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/helitronscanner:1.0--hdfd78af_0': + 'biocontainers/helitronscanner:1.0--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(head) + tuple val(meta3), path(tail) + + output: + tuple val(meta), path("*.draw") , emit: draw + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ( !task.memory ) { error '[HELITRONSCANNER_DRAW] Available memory not known. Specify process memory requirements to fix this.' } + def avail_mem = (task.memory.giga*0.8).intValue() + """ + # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) + # Check for container variable initialisation script and source it. + if [ -f "/usr/local/env-activate.sh" ]; then + set +u # Otherwise, errors out because of various unbound variables + . "/usr/local/env-activate.sh" + set -u + fi + + HelitronScanner \\ + pairends \\ + -Xmx${avail_mem}g \\ + -head_score $head \\ + -tail_score $tail \\ + -output ${prefix}.pairends \\ + ${args2} + + HelitronScanner \\ + draw \\ + -Xmx${avail_mem}g \\ + -pscore ${prefix}.pairends \\ + -g $fasta \\ + -output ${prefix}.draw \\ + ${args} + + mv ${prefix}.draw.hel.fa \\ + ${prefix}.draw + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.draw + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ +} diff --git a/modules/gallvp/helitronscanner/draw/meta.yml b/modules/gallvp/helitronscanner/draw/meta.yml new file mode 100644 index 0000000..96bd260 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/meta.yml @@ -0,0 +1,69 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "helitronscanner_draw" +description: HelitronScanner draw tool for Helitron transposons in genomes +keywords: + - genomics + - helitron + - scanner +tools: + - "helitronscanner": + description: "HelitronScanner uncovers a large overlooked cache of Helitron transposons + in many genomes" + homepage: "https://sourceforge.net/projects/helitronscanner" + documentation: "https://sourceforge.net/projects/helitronscanner" + tool_dev_url: "https://sourceforge.net/projects/helitronscanner" + doi: "10.1073/pnas.1410068111" + licence: ["GPL v3-or-later"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome data to scan for Helitrons + pattern: "*.{fa,fsa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - head: + type: file + description: Output of the HelitronScanner head command + pattern: "*.head" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tail: + type: file + description: Output of the HelitronScanner tail command + pattern: "*.tail" +output: + - draw: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.draw" + - "*.draw": + type: map + description: | + The draw output from HelitronScanner + pattern: "*.draw" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" + - "@jguhlin" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/helitronscanner/draw/tests/main.nf.test b/modules/gallvp/helitronscanner/draw/tests/main.nf.test new file mode 100644 index 0000000..331f563 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/main.nf.test @@ -0,0 +1,159 @@ +nextflow_process { + + name "Test Process HELITRONSCANNER_DRAW" + script "../main.nf" + config "./nextflow.config" + process "HELITRONSCANNER_DRAW" + + tag "modules" + tag "modules_gallvp" + tag "helitronscanner" + tag "helitronscanner/draw" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANHEAD') { + script "../../scan/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANTAIL') { + script "../../scan/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + } + + test("actinidia_chinensis-genome_1_fasta_gz-success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = HELITRONSCANNER_SCANHEAD.out.scan + input[2] = HELITRONSCANNER_SCANTAIL.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("sarscov2 - genome - success") { + + setup { + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANHEAD_SARSCOV2') { + script "../../scan/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + run('HELITRONSCANNER_SCAN', alias: 'HELITRONSCANNER_SCANTAIL_SARSCOV2') { + script "../../scan/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = HELITRONSCANNER_SCANHEAD_SARSCOV2.out.scan + input[2] = HELITRONSCANNER_SCANTAIL_SARSCOV2.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.draw[0][1] != null }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = HELITRONSCANNER_SCANHEAD.out.scan + input[2] = HELITRONSCANNER_SCANTAIL.out.scan + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap b/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap new file mode 100644 index 0000000..208d14d --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/main.nf.test.snap @@ -0,0 +1,80 @@ +{ + "actinidia_chinensis-genome_1_fasta_gz-success": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "1": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ], + "draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "versions": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:51:49.477212" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ], + "draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:52:47.744899" + }, + "sarscov2 - genome - success": { + "content": [ + [ + "versions.yml:md5,4b206968a702782fa04d2ba560c89728" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:58:21.800568" + } +} \ No newline at end of file diff --git a/modules/gallvp/helitronscanner/draw/tests/nextflow.config b/modules/gallvp/helitronscanner/draw/tests/nextflow.config new file mode 100644 index 0000000..57f4900 --- /dev/null +++ b/modules/gallvp/helitronscanner/draw/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } +} diff --git a/modules/gallvp/helitronscanner/scan/environment.yml b/modules/gallvp/helitronscanner/scan/environment.yml new file mode 100644 index 0000000..ea89d39 --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::helitronscanner=1.0" diff --git a/modules/gallvp/helitronscanner/scan/main.nf b/modules/gallvp/helitronscanner/scan/main.nf new file mode 100644 index 0000000..0f748ab --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/main.nf @@ -0,0 +1,72 @@ +process HELITRONSCANNER_SCAN { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/helitronscanner:1.0--hdfd78af_0': + 'biocontainers/helitronscanner:1.0--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + val command + path lcv_filepath + val buffer_size + + output: + tuple val(meta), path("*.$command") , emit: scan + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + if ( command !in [ 'head', 'tail' ] ) error "[HELITRONSCANNER_SCAN] command argument should be 'head' or 'tail'" + if ( !task.memory ) { error '[HELITRONSCANNER_SCAN] Available memory not known. Specify process memory requirements to fix this.' } + + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def is_head = { command == 'head' }() + def subcommand = is_head ? 'scanHead' : 'scanTail' + def lcvs_file = is_head ? 'head.lcvs' : 'tail.lcvs' + def lcv_arg = lcv_filepath ? "-lcv_filepath $lcv_filepath" : "-lcv_filepath \$HELITRONSCANNER_TRAININGSET_PATH/$lcvs_file" + def avail_mem = (task.memory.giga*0.8).intValue() + """ + # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) + # Check for container variable initialisation script and source it. + if [ -f "/usr/local/env-activate.sh" ]; then + set +u # Otherwise, errors out because of various unbound variables + . "/usr/local/env-activate.sh" + set -u + fi + + HelitronScanner \\ + $subcommand \\ + -Xmx${avail_mem}g \\ + $lcv_arg \\ + -genome $fasta \\ + -buffer_size $buffer_size \\ + -threads_LCV $task.cpus \\ + $args \\ + -output ${prefix}.${command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ + + stub: + if ( command !in [ 'head', 'tail' ] ) error "[HELITRONSCANNER_SCAN] command argument should be 'head' or 'tail'" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.${command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + helitronscanner: \$(HelitronScanner |& sed -n 's/HelitronScanner V\\(.*\\)/V\\1/p') + END_VERSIONS + """ +} diff --git a/modules/gallvp/helitronscanner/scan/meta.yml b/modules/gallvp/helitronscanner/scan/meta.yml new file mode 100644 index 0000000..ed8f956 --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/meta.yml @@ -0,0 +1,60 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "helitronscanner_scan" +description: HelitronScanner scanHead and scanTail tools for Helitron transposons + in genomes +keywords: + - genomics + - helitron + - scanner +tools: + - "helitronscanner": + description: "HelitronScanner uncovers a large overlooked cache of Helitron transposons + in many genomes" + homepage: "https://sourceforge.net/projects/helitronscanner" + documentation: "https://sourceforge.net/projects/helitronscanner" + tool_dev_url: "https://sourceforge.net/projects/helitronscanner" + doi: "10.1073/pnas.1410068111" + licence: ["GPL v3-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome data to scan for Helitrons + pattern: "*.{fa,fsa,fasta}" + - - command: + type: string + description: Command to execute. One of [ 'head', 'tail' ] + - - lcv_filepath: + type: file + description: LCV file path. If not provided by setting it to [], the LCV file + packaged with the module will be used + pattern: "*.lcvs" + - - buffer_size: + type: integer + description: Genome slice size (use negative or zero for non-buffer, i.e. treat + every whole chromosome) +output: + - scan: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.$command": + type: file + description: Head or tail file depending on the command + pattern: "*.$command" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/helitronscanner/scan/tests/main.nf.test b/modules/gallvp/helitronscanner/scan/tests/main.nf.test new file mode 100644 index 0000000..55bcfed --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/tests/main.nf.test @@ -0,0 +1,148 @@ +nextflow_process { + + name "Test Process HELITRONSCANNER_SCAN" + script "../main.nf" + process "HELITRONSCANNER_SCAN" + + tag "modules" + tag "modules_gallvp" + tag "helitronscanner" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + } + + test("actinidia_chinensis - genome_1_fasta_gz - head - success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('2729827:1 2729980:1 2730005:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("actinidia_chinensis - genome_1_fasta_gz - tail - success") { + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('7265:1 7951:1 9264:2 9398:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("sarscov2 - genome - head - success") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.scan[0][1]).text.contains('113:2 236:1 1158:1 1754:2 1771:1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'head' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stub - tail") { + + options "-stub" + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = 'tail' + input[2] = [] + input[3] = 0 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap b/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap new file mode 100644 index 0000000..ac7ae5e --- /dev/null +++ b/modules/gallvp/helitronscanner/scan/tests/main.nf.test.snap @@ -0,0 +1,104 @@ +{ + "actinidia_chinensis - genome_1_fasta_gz - tail - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:51:54.403269" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.head:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ], + "scan": [ + [ + { + "id": "test" + }, + "test.head:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:52:10.250343" + }, + "sarscov2 - genome - head - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:43:05.068944" + }, + "stub - tail": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tail:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ], + "scan": [ + [ + { + "id": "test" + }, + "test.tail:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:39:42.225262" + }, + "actinidia_chinensis - genome_1_fasta_gz - head - success": { + "content": [ + [ + "versions.yml:md5,3c675f4be863f58c88db5a2936beaa88" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T11:51:18.942428" + } +} \ No newline at end of file diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf new file mode 100644 index 0000000..40c2541 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf @@ -0,0 +1,86 @@ +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_DRAW } from '../../../modules/gallvp/helitronscanner/draw/main.nf' + +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD_RC } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL_RC } from '../../../modules/gallvp/helitronscanner/scan/main.nf' +include { HELITRONSCANNER_DRAW as HELITRONSCANNER_DRAW_RC } from '../../../modules/gallvp/helitronscanner/draw/main.nf' + +workflow FASTA_HELITRONSCANNER_SCAN_DRAW { + + take: + ch_fasta // channel: [ val(meta), fasta ] + + main: + + ch_versions = Channel.empty() + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD + HELITRONSCANNER_SCAN_HEAD ( + ch_fasta, + 'head', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_head = HELITRONSCANNER_SCAN_HEAD.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_HEAD.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL + HELITRONSCANNER_SCAN_TAIL ( + ch_fasta, + 'tail', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_tail = HELITRONSCANNER_SCAN_TAIL.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_TAIL.out.versions) + + // MODULE: HELITRONSCANNER_DRAW + HELITRONSCANNER_DRAW ( + ch_fasta, + ch_helitronscanner_scan_head, + ch_helitronscanner_scan_tail + ) + + ch_helitronscanner_draw = HELITRONSCANNER_DRAW.out.draw + ch_versions = ch_versions.mix(HELITRONSCANNER_DRAW.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_HEAD_RC + HELITRONSCANNER_SCAN_HEAD_RC ( + ch_fasta, + 'head', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_head_rc = HELITRONSCANNER_SCAN_HEAD_RC.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_HEAD_RC.out.versions) + + // MODULE: HELITRONSCANNER_SCAN as HELITRONSCANNER_SCAN_TAIL_RC + HELITRONSCANNER_SCAN_TAIL_RC ( + ch_fasta, + 'tail', // command + [], // lcv_filepath + 0 // buffer_size + ) + + ch_helitronscanner_scan_tail_rc = HELITRONSCANNER_SCAN_TAIL_RC.out.scan + ch_versions = ch_versions.mix(HELITRONSCANNER_SCAN_TAIL_RC.out.versions) + + // MODULE: HELITRONSCANNER_DRAW as HELITRONSCANNER_DRAW_RC + HELITRONSCANNER_DRAW_RC ( + ch_fasta, + ch_helitronscanner_scan_head_rc, + ch_helitronscanner_scan_tail_rc + ) + + ch_helitronscanner_draw_rc = HELITRONSCANNER_DRAW_RC.out.draw + ch_versions = ch_versions.mix(HELITRONSCANNER_DRAW_RC.out.versions) + + emit: + helitronscanner_draw = ch_helitronscanner_draw // channel: [ val(meta), draw ] + helitronscanner_draw_rc = ch_helitronscanner_draw_rc // channel: [ val(meta), rc.draw ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml new file mode 100644 index 0000000..62c4b39 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/meta.yml @@ -0,0 +1,45 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fasta_helitronscanner_scan_draw" +description: Find helitrons suing Helitronscanner scan, pairends and draw subcommands +keywords: + - helitron + - scan + - draw + - pairends + - repeat + - genomics + - fasta +components: + - helitronscanner/scan + - helitronscanner/draw +input: + - ch_fasta: + type: file + description: | + Genome fasta + Structure: [ val(meta), fasta ] + pattern: "*.fasta" +output: + - helitronscanner_draw: + type: file + description: | + Helitronscanner draw file + Structure: [ val(meta), draw ] + pattern: "*.draw" + - helitronscanner_draw_rc: + type: file + description: | + Helitronscanner reverse complement draw file + Structure: [ val(meta), rc.draw ] + pattern: "*.rc.draw" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" + - "@jguhlin" diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test new file mode 100644 index 0000000..7a9bd05 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test @@ -0,0 +1,97 @@ +nextflow_workflow { + + name "Test Subworkflow FASTA_HELITRONSCANNER_SCAN_DRAW" + script "../main.nf" + workflow "FASTA_HELITRONSCANNER_SCAN_DRAW" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_gallvp" + tag "subworkflows/fasta_helitronscanner_scan_draw" + + tag "helitronscanner/draw" + tag "helitronscanner/scan" + tag "gunzip" + + setup { + run('GUNZIP') { + script "../../../../modules/gallvp/gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + } + + test("actinidia_chinensis - genome_1_fasta_gz") { + + when { + workflow { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } + + test("sarscov2 - genome") { + + when { + workflow { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.out.helitronscanner_draw }, // empty + { assert workflow.out.helitronscanner_draw_rc }, // empty + { assert snapshot( + workflow.out.versions + ).match() + } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } +} diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap new file mode 100644 index 0000000..f6b8077 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/main.nf.test.snap @@ -0,0 +1,137 @@ +{ + "actinidia_chinensis - genome_1_fasta_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,7aeed0fdf50f8cb2516b2e92f456835e" + ] + ], + "2": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ], + "helitronscanner_draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,434aaaa70c294464e6bae93b2895b13c" + ] + ], + "helitronscanner_draw_rc": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,7aeed0fdf50f8cb2516b2e92f456835e" + ] + ], + "versions": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T11:53:51.717511" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ], + "helitronscanner_draw": [ + [ + { + "id": "test" + }, + "test.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "helitronscanner_draw_rc": [ + [ + { + "id": "test" + }, + "test.rc.draw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T11:54:17.824589" + }, + "sarscov2 - genome": { + "content": [ + [ + "versions.yml:md5,42ab90da7ef86125b9dec685f4f08e84", + "versions.yml:md5,9b6a0f2f56d89451cf16702e2f358520", + "versions.yml:md5,a928ae7c94a23e5c62c27915dada660c", + "versions.yml:md5,c417497b1caea1cd51f8440df92daa40", + "versions.yml:md5,d786d80e914a86ce0361cfc0bc62cda9", + "versions.yml:md5,f3b6aa20e81f04fd731fad64f7ea3c14" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-21T12:03:43.135817" + } +} \ No newline at end of file diff --git a/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config new file mode 100644 index 0000000..b98d370 --- /dev/null +++ b/subworkflows/gallvp/fasta_helitronscanner_scan_draw/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + withName: 'HELITRONSCANNER_DRAW' { + ext.args = '-pure_helitron' + } + + withName: 'HELITRONSCANNER_SCAN_HEAD_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'HELITRONSCANNER_SCAN_TAIL_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '--rc' + } + + withName: 'HELITRONSCANNER_DRAW_RC' { + ext.prefix = { "${meta.id}.rc" } + ext.args = '-pure_helitron' + } +} diff --git a/workflows/edta.nf b/workflows/edta.nf index df8b2d9..357b427 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -1,14 +1,15 @@ -include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' -include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' -include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' -include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' - -include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' +include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' +include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' + +include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' workflow EDTA { @@ -124,6 +125,9 @@ workflow EDTA { ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW + FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) + // Function: Save versions ch_versions = ch_versions From 5a874e79e64c30db9bc83126fb8a8880544b42c2 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 26 Nov 2024 22:39:10 +1300 Subject: [PATCH 23/49] Updated snapshots --- conf/modules.config | 8 ++++---- test/nf-test/small/main.nf.test.snap | 22 ++++++++++++++++++++-- test/nf-test/tiny/main.nf.test.snap | 22 ++++++++++++++++++++-- workflows/edta.nf | 4 ++++ 4 files changed, 48 insertions(+), 8 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e70a6ea..39b1af8 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -20,21 +20,21 @@ process { ext.args = '-engine ncbi' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { ext.args = '-pure_helitron' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA::FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '-pure_helitron' } diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap index d53e834..9154059 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/test/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 9, + "successful tasks": 15, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,24 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "HELITRONSCANNER_DRAW": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_DRAW_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL_RC": { + "helitronscanner": "V1.1" + }, "LTRFINDER": { "LTR_FINDER_parallel": "v1.1", "ltr_finder": "v1.07" @@ -43,6 +61,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-25T13:53:22.07666" + "timestamp": "2024-11-26T22:38:20.031297" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap index a61631f..946ed5d 100644 --- a/test/nf-test/tiny/main.nf.test.snap +++ b/test/nf-test/tiny/main.nf.test.snap @@ -2,7 +2,7 @@ "tiny genome": { "content": [ { - "successful tasks": 7, + "successful tasks": 13, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,24 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "HELITRONSCANNER_DRAW": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_DRAW_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_HEAD_RC": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL": { + "helitronscanner": "V1.1" + }, + "HELITRONSCANNER_SCAN_TAIL_RC": { + "helitronscanner": "V1.1" + }, "LTRFINDER": { "LTR_FINDER_parallel": "v1.1", "ltr_finder": "v1.07" @@ -37,6 +55,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.1" }, - "timestamp": "2024-11-25T13:20:57.770583" + "timestamp": "2024-11-26T22:35:05.489004" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index 357b427..cf99f9f 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -128,6 +128,10 @@ workflow EDTA { // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) + ch_helitronscanner_draw = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw + ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc + ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) + // Function: Save versions ch_versions = ch_versions From d2feab0390bfd416f381b9b98fdc907171ecc6f8 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 28 Nov 2024 18:25:55 +1300 Subject: [PATCH 24/49] Added CLEANUP_TANDEM --- bin/cleanup_tandem.pl | 0 modules/local/cleanup_tandem/environment.yml | 8 +++ modules/local/cleanup_tandem/main.nf | 49 +++++++++++++ .../local/cleanup_tandem/tests/main.nf.test | 56 +++++++++++++++ .../cleanup_tandem/tests/main.nf.test.snap | 68 +++++++++++++++++++ 5 files changed, 181 insertions(+) mode change 100644 => 100755 bin/cleanup_tandem.pl create mode 100644 modules/local/cleanup_tandem/environment.yml create mode 100644 modules/local/cleanup_tandem/main.nf create mode 100644 modules/local/cleanup_tandem/tests/main.nf.test create mode 100644 modules/local/cleanup_tandem/tests/main.nf.test.snap diff --git a/bin/cleanup_tandem.pl b/bin/cleanup_tandem.pl old mode 100644 new mode 100755 diff --git a/modules/local/cleanup_tandem/environment.yml b/modules/local/cleanup_tandem/environment.yml new file mode 100644 index 0000000..8d38804 --- /dev/null +++ b/modules/local/cleanup_tandem/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::trf=4.09.1" + - "conda-forge::perl=5.32.1" \ No newline at end of file diff --git a/modules/local/cleanup_tandem/main.nf b/modules/local/cleanup_tandem/main.nf new file mode 100644 index 0000000..ae84cd2 --- /dev/null +++ b/modules/local/cleanup_tandem/main.nf @@ -0,0 +1,49 @@ +process CLEANUP_TANDEM { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'community.wave.seqera.io/library/trf_perl:44f9844b1bf765c3' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.fasta") , emit: cleaned_fasta + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + if ( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + cleanup_tandem.pl \\ + -f $fasta \\ + $args \\ + > ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ( "$fasta" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/cleanup_tandem/tests/main.nf.test b/modules/local/cleanup_tandem/tests/main.nf.test new file mode 100644 index 0000000..b13870e --- /dev/null +++ b/modules/local/cleanup_tandem/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process CLEANUP_TANDEM" + script "../main.nf" + process "CLEANUP_TANDEM" + + tag "cleanup_tandem" + tag "modules_local" + tag "modules" + + test("sarscov2 - genome") { + + when { + process { + """ + input[0] = [ + [ id: 'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - genome - stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/local/cleanup_tandem/tests/main.nf.test.snap b/modules/local/cleanup_tandem/tests/main.nf.test.snap new file mode 100644 index 0000000..a36d60e --- /dev/null +++ b/modules/local/cleanup_tandem/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - genome - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ], + "cleaned_fasta": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-28T16:12:53.161124" + }, + "sarscov2 - genome": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,e73599798195a519ba2565c3f0275b93" + ] + ], + "1": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ], + "cleaned_fasta": [ + [ + { + "id": "sarscov2" + }, + "sarscov2.fasta:md5,e73599798195a519ba2565c3f0275b93" + ] + ], + "versions": [ + "versions.yml:md5,2cce04ed211ff9c6f7f322d2b217af83" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-28T16:12:48.160979" + } +} \ No newline at end of file From 1d99e2a2e7f9d9c700b4e880a7c1de1c633b2e52 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 21 Nov 2024 11:51:55 +1300 Subject: [PATCH 25/49] Initial try on format_helitronscanner --- .../format_helitronscanner/environment.yml | 7 +++ modules/local/format_helitronscanner/main.nf | 55 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 modules/local/format_helitronscanner/environment.yml create mode 100644 modules/local/format_helitronscanner/main.nf diff --git a/modules/local/format_helitronscanner/environment.yml b/modules/local/format_helitronscanner/environment.yml new file mode 100644 index 0000000..d2f633e --- /dev/null +++ b/modules/local/format_helitronscanner/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner/main.nf b/modules/local/format_helitronscanner/main.nf new file mode 100644 index 0000000..9d41ab6 --- /dev/null +++ b/modules/local/format_helitronscanner/main.nf @@ -0,0 +1,55 @@ +process FORMAT_HELITRONSCANNER_OUT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1': + 'biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" + + input: + tuple val(meta), path(genome) + path hel_fa // HelitronScanner.draw.hel.fa file + path rc_hel_fa // HelitronScanner.draw.rc.hel.fa file + + output: + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.tabout"), emit: filtered_tabout + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.fa"), emit: filtered_fa, optional: true + tuple val(meta), path("${meta.id}.HelitronScanner.filtered.ext.fa"), emit: filtered_ext_fa, optional: true + tuple val(meta), path("${meta.id}.format_helitronscanner_out.log"), emit: log + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Set default values for the optional arguments + def sitefilter = task.ext.sitefilter != null ? task.ext.sitefilter : 1 + def minscore = task.ext.minscore != null ? task.ext.minscore : 12 + def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 + def extlen = task.ext.extlen != null ? task.ext.extlen : 30 + def extout = task.ext.extout != null ? task.ext.extout : 1 + def prefix = meta.id + + """ + # Create symbolic links to match expected filenames + ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa + ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa + + # Run the Perl script with the provided arguments + perl format_helitronscanner_out.pl \\ + -genome $genome \\ + -sitefilter $sitefilter \\ + -minscore $minscore \\ + -keepshorter $keepshorter \\ + -extlen $extlen \\ + -extout $extout \\ + &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) + + # Capture version information + cat <<-END_VERSIONS > versions.yml + "${task.process}": + Perl: \$(perl -v | grep 'This is perl' | awk '{print \$4}') + END_VERSIONS + """ +} From 30c2fd6990c7164f09a1bd37dd3dac80486b80de Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 11:36:13 +1300 Subject: [PATCH 26/49] Make changes suggested by @GallVp --- .../environment.yml | 0 .../main.nf | 7 +++---- 2 files changed, 3 insertions(+), 4 deletions(-) rename modules/local/{format_helitronscanner => format_helitronscanner_out}/environment.yml (100%) rename modules/local/{format_helitronscanner => format_helitronscanner_out}/main.nf (91%) diff --git a/modules/local/format_helitronscanner/environment.yml b/modules/local/format_helitronscanner_out/environment.yml similarity index 100% rename from modules/local/format_helitronscanner/environment.yml rename to modules/local/format_helitronscanner_out/environment.yml diff --git a/modules/local/format_helitronscanner/main.nf b/modules/local/format_helitronscanner_out/main.nf similarity index 91% rename from modules/local/format_helitronscanner/main.nf rename to modules/local/format_helitronscanner_out/main.nf index 9d41ab6..2364644 100644 --- a/modules/local/format_helitronscanner/main.nf +++ b/modules/local/format_helitronscanner_out/main.nf @@ -29,14 +29,14 @@ process FORMAT_HELITRONSCANNER_OUT { def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 def extlen = task.ext.extlen != null ? task.ext.extlen : 30 def extout = task.ext.extout != null ? task.ext.extout : 1 - def prefix = meta.id + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' """ # Create symbolic links to match expected filenames ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa - # Run the Perl script with the provided arguments perl format_helitronscanner_out.pl \\ -genome $genome \\ -sitefilter $sitefilter \\ @@ -46,10 +46,9 @@ process FORMAT_HELITRONSCANNER_OUT { -extout $extout \\ &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) - # Capture version information cat <<-END_VERSIONS > versions.yml "${task.process}": - Perl: \$(perl -v | grep 'This is perl' | awk '{print \$4}') + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') END_VERSIONS """ } From 1f35229c5dcb07c0e6805d0bf4febff0978166c2 Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 11:49:23 +1300 Subject: [PATCH 27/49] Added some tests - not yet working, need the nf-test.config from the existing PR --- .../tests/environment.yml | 7 ++ .../tests/main.nf.test | 90 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 modules/local/format_helitronscanner_out/tests/environment.yml create mode 100644 modules/local/format_helitronscanner_out/tests/main.nf.test diff --git a/modules/local/format_helitronscanner_out/tests/environment.yml b/modules/local/format_helitronscanner_out/tests/environment.yml new file mode 100644 index 0000000..d2f633e --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test new file mode 100644 index 0000000..d1808cd --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process FORMAT_HELITRONSCANNER_OUT" + script "../main.nf" + process "FORMAT_HELITRONSCANNER_OUT" + + tag "modules" + tag "modules_nfcore" + tag "format_helitronscanner_out" + + test("homo_sapiens - genome_21_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.filtered_tabout, + process.out.log + process.out.versions + ).match() + }, + { assert path(process.out.filtered_tabout[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") }, + ) + } + + } + + test("sarscov2 - genome_fasta - no helitrons") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gff3, + process.out.versions + ).match() + }, + { assert path(process.out.filtered_tabout[0][1]).text.contains("predictions are reported in the following way") }, + ) + } + + } + + test("homo_sapiens - genome_fasta - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} From 1fb9dd2241c9411384376d82677a12d569db181c Mon Sep 17 00:00:00 2001 From: Joseph Guhlin Date: Thu, 28 Nov 2024 12:11:23 +1300 Subject: [PATCH 28/49] Typo --- modules/local/format_helitronscanner_out/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test index d1808cd..5745153 100644 --- a/modules/local/format_helitronscanner_out/tests/main.nf.test +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -26,7 +26,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.filtered_tabout, - process.out.log + process.out.log, process.out.versions ).match() }, From fde5ef376f0362b65319458f2f790171dae8a76a Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 3 Dec 2024 14:33:19 +1300 Subject: [PATCH 29/49] Incorporated FORMAT_HELITRONSCANNER_OUT --- bin/format_helitronscanner_out.pl | 0 conf/modules.config | 4 ++ .../environment.yml | 2 +- .../local/format_helitronscanner_out/main.nf | 49 +++++++------- .../tests/environment.yml | 7 -- .../tests/main.nf.test | 65 ++----------------- .../tests/main.nf.test.snap | 63 ++++++++++++++++++ test/nf-test/small/main.nf.test.snap | 9 ++- test/nf-test/tiny/main.nf.test.snap | 9 ++- workflows/edta.nf | 19 ++++++ 10 files changed, 130 insertions(+), 97 deletions(-) mode change 100644 => 100755 bin/format_helitronscanner_out.pl delete mode 100644 modules/local/format_helitronscanner_out/tests/environment.yml create mode 100644 modules/local/format_helitronscanner_out/tests/main.nf.test.snap diff --git a/bin/format_helitronscanner_out.pl b/bin/format_helitronscanner_out.pl old mode 100644 new mode 100755 diff --git a/conf/modules.config b/conf/modules.config index 39b1af8..918b569 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -38,5 +38,9 @@ process { ext.prefix = { "${meta.id}.rc" } ext.args = '-pure_helitron' } + + withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { + ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' + } } \ No newline at end of file diff --git a/modules/local/format_helitronscanner_out/environment.yml b/modules/local/format_helitronscanner_out/environment.yml index d2f633e..b6205eb 100644 --- a/modules/local/format_helitronscanner_out/environment.yml +++ b/modules/local/format_helitronscanner_out/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::perl-bioperl=1.7.8" + - "conda-forge::perl=5.32.1" diff --git a/modules/local/format_helitronscanner_out/main.nf b/modules/local/format_helitronscanner_out/main.nf index 2364644..ebfe998 100644 --- a/modules/local/format_helitronscanner_out/main.nf +++ b/modules/local/format_helitronscanner_out/main.nf @@ -4,46 +4,35 @@ process FORMAT_HELITRONSCANNER_OUT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1': - 'biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0905ae7aa2a1c4135b448b49dd205b4eb370d4733b832594563ee06832ebd09/data': + 'community.wave.seqera.io/library/perl:67db1a8d53d64b14' }" input: tuple val(meta), path(genome) - path hel_fa // HelitronScanner.draw.hel.fa file - path rc_hel_fa // HelitronScanner.draw.rc.hel.fa file + path hel_fa + path rc_hel_fa output: - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.tabout"), emit: filtered_tabout - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.fa"), emit: filtered_fa, optional: true - tuple val(meta), path("${meta.id}.HelitronScanner.filtered.ext.fa"), emit: filtered_ext_fa, optional: true - tuple val(meta), path("${meta.id}.format_helitronscanner_out.log"), emit: log - path "versions.yml", emit: versions + tuple val(meta), path("*.HelitronScanner.filtered.tabout") , emit: filtered_tabout + tuple val(meta), path("*.HelitronScanner.filtered.fa") , emit: filtered_fa , optional: true + tuple val(meta), path("*.HelitronScanner.filtered.ext.fa") , emit: filtered_ext_fa , optional: true + tuple val(meta), path("*.format_helitronscanner_out.log") , emit: log + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - // Set default values for the optional arguments - def sitefilter = task.ext.sitefilter != null ? task.ext.sitefilter : 1 - def minscore = task.ext.minscore != null ? task.ext.minscore : 12 - def keepshorter = task.ext.keepshorter != null ? task.ext.keepshorter : 1 - def extlen = task.ext.extlen != null ? task.ext.extlen : 30 - def extout = task.ext.extout != null ? task.ext.extout : 1 - def prefix = task.ext.prefix ?: "${meta.id}" - def args = task.ext.args ?: '' - + def prefix = task.ext.prefix ?: "$genome" + def args = task.ext.args ?: '' """ # Create symbolic links to match expected filenames ln -s $hel_fa ${genome}.HelitronScanner.draw.hel.fa ln -s $rc_hel_fa ${genome}.HelitronScanner.draw.rc.hel.fa - perl format_helitronscanner_out.pl \\ + format_helitronscanner_out.pl \\ -genome $genome \\ - -sitefilter $sitefilter \\ - -minscore $minscore \\ - -keepshorter $keepshorter \\ - -extlen $extlen \\ - -extout $extout \\ + $args \\ &> >(tee "${prefix}.format_helitronscanner_out.log" 2>&1) cat <<-END_VERSIONS > versions.yml @@ -51,4 +40,16 @@ process FORMAT_HELITRONSCANNER_OUT { perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "$genome" + """ + touch ${prefix}.HelitronScanner.filtered.tabout + touch ${prefix}.format_helitronscanner_out.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + END_VERSIONS + """ } diff --git a/modules/local/format_helitronscanner_out/tests/environment.yml b/modules/local/format_helitronscanner_out/tests/environment.yml deleted file mode 100644 index d2f633e..0000000 --- a/modules/local/format_helitronscanner_out/tests/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - "bioconda::perl-bioperl=1.7.8" diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test b/modules/local/format_helitronscanner_out/tests/main.nf.test index 5745153..864bc15 100644 --- a/modules/local/format_helitronscanner_out/tests/main.nf.test +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test @@ -5,65 +5,10 @@ nextflow_process { process "FORMAT_HELITRONSCANNER_OUT" tag "modules" - tag "modules_nfcore" + tag "modules_local" tag "format_helitronscanner_out" - test("homo_sapiens - genome_21_fasta") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.filtered_tabout, - process.out.log, - process.out.versions - ).match() - }, - { assert path(process.out.filtered_tabout[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") }, - ) - } - - } - - test("sarscov2 - genome_fasta - no helitrons") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.gff3, - process.out.versions - ).match() - }, - { assert path(process.out.filtered_tabout[0][1]).text.contains("predictions are reported in the following way") }, - ) - } - - } - - test("homo_sapiens - genome_fasta - stub") { + test("sarscov2 - genome_fasta - stub") { options '-stub' @@ -71,9 +16,11 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[1] = [] + input[2] = [] """ } } diff --git a/modules/local/format_helitronscanner_out/tests/main.nf.test.snap b/modules/local/format_helitronscanner_out/tests/main.nf.test.snap new file mode 100644 index 0000000..9079015 --- /dev/null +++ b/modules/local/format_helitronscanner_out/tests/main.nf.test.snap @@ -0,0 +1,63 @@ +{ + "sarscov2 - genome_fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.HelitronScanner.filtered.tabout:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.format_helitronscanner_out.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,250d1a5d5f60868f6cf0f17bd52edd91" + ], + "filtered_ext_fa": [ + + ], + "filtered_fa": [ + + ], + "filtered_tabout": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.HelitronScanner.filtered.tabout:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "sarscov2" + }, + "genome.fasta.format_helitronscanner_out.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,250d1a5d5f60868f6cf0f17bd52edd91" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-12-03T14:26:36.313536" + } +} \ No newline at end of file diff --git a/test/nf-test/small/main.nf.test.snap b/test/nf-test/small/main.nf.test.snap index 9154059..5a164b2 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/test/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 15, + "successful tasks": 16, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,9 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "FORMAT_HELITRONSCANNER_OUT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, @@ -59,8 +62,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-11-26T22:38:20.031297" + "timestamp": "2024-12-03T14:20:03.748125" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test.snap b/test/nf-test/tiny/main.nf.test.snap index 946ed5d..20a57ef 100644 --- a/test/nf-test/tiny/main.nf.test.snap +++ b/test/nf-test/tiny/main.nf.test.snap @@ -2,7 +2,7 @@ "tiny genome": { "content": [ { - "successful tasks": 13, + "successful tasks": 14, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,9 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "FORMAT_HELITRONSCANNER_OUT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, @@ -53,8 +56,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-11-26T22:35:05.489004" + "timestamp": "2024-12-03T14:16:25.986375" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index cf99f9f..05a6da3 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -8,6 +8,7 @@ include { ANNOSINE } from '../modules/gallvp/annosine/m include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' +include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' @@ -132,6 +133,24 @@ workflow EDTA { ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) + // MODULE: FORMAT_HELITRONSCANNER_OUT + ch_format_helitronscanner_inputs = ch_sanitized_fasta + | join(ch_helitronscanner_draw) + | join(ch_helitronscanner_draw_rc) + | multiMap { meta, fasta, draw, draw_rc -> + genome: [ meta, fasta ] + hel_fa: draw + rc_hel_fa: draw_rc + } + + FORMAT_HELITRONSCANNER_OUT ( + ch_format_helitronscanner_inputs.genome, + ch_format_helitronscanner_inputs.hel_fa, + ch_format_helitronscanner_inputs.rc_hel_fa, + ) + + ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) + // Function: Save versions ch_versions = ch_versions From 41683a77682b23bc8c101147e83131c2ef69d487 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 13:21:56 +1300 Subject: [PATCH 30/49] Renamed test to tests to avoid meta.id conflicts in nf-test and added LTR_RETRIEVER_POSTPROCESS --- .github/check_binaries.sh | 12 + .github/workflows/linting.yml | 20 + .pre-commit-config.yaml | 11 + bin/EDTA_raw.pl | 761 ++++++++++++++++++ bin/setup_LTR_retriever_postprocess.sh | 26 + conf/modules.config | 10 + conf/test.config | 2 +- .../ltr_retriever_postprocess/environment.yml | 10 + .../local/ltr_retriever_postprocess/main.nf | 80 ++ .../nf-core/ltrretriever/ltrretriever/main.nf | 96 +++ .../ltrretriever/tests/main.nf.test.snap | 160 ++++ nextflow.config | 4 + nf-test.config | 2 +- {test => tests}/Alyrata.test.fa | 0 {test => tests}/Col.test.fa | 0 {test => tests}/Ler.test.fa | 0 {test => tests}/README.txt | 0 {test => tests}/genome.cds.fa | 0 {test => tests}/genome.cds.list | 0 {test => tests}/genome.exclude.bed | 0 {test => tests}/genome.fa | 0 {test => tests}/nf-test/nextflow.config | 0 {test => tests}/nf-test/small/main.nf.test | 26 +- .../nf-test/small/main.nf.test.snap | 21 +- {test => tests}/nf-test/tiny/main.nf.test | 0 .../nf-test/tiny/main.nf.test.snap | 0 workflows/edta.nf | 44 +- 27 files changed, 1271 insertions(+), 14 deletions(-) create mode 100755 .github/check_binaries.sh create mode 100644 .github/workflows/linting.yml create mode 100644 .pre-commit-config.yaml create mode 100755 bin/EDTA_raw.pl create mode 100755 bin/setup_LTR_retriever_postprocess.sh create mode 100644 modules/local/ltr_retriever_postprocess/environment.yml create mode 100644 modules/local/ltr_retriever_postprocess/main.nf create mode 100644 modules/nf-core/ltrretriever/ltrretriever/main.nf create mode 100644 modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap rename {test => tests}/Alyrata.test.fa (100%) rename {test => tests}/Col.test.fa (100%) rename {test => tests}/Ler.test.fa (100%) rename {test => tests}/README.txt (100%) rename {test => tests}/genome.cds.fa (100%) rename {test => tests}/genome.cds.list (100%) rename {test => tests}/genome.exclude.bed (100%) rename {test => tests}/genome.fa (100%) rename {test => tests}/nf-test/nextflow.config (100%) rename {test => tests}/nf-test/small/main.nf.test (50%) rename {test => tests}/nf-test/small/main.nf.test.snap (72%) rename {test => tests}/nf-test/tiny/main.nf.test (100%) rename {test => tests}/nf-test/tiny/main.nf.test.snap (100%) diff --git a/.github/check_binaries.sh b/.github/check_binaries.sh new file mode 100755 index 0000000..79e8784 --- /dev/null +++ b/.github/check_binaries.sh @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +set -euo pipefail + +EDTA_raw_pl_version=$(md5sum EDTA_raw.pl | cut -f1 -d' ') +bin_EDTA_raw_pl_version=$(md5sum bin/EDTA_raw.pl | cut -f1 -d' ') + +if [[ $EDTA_raw_pl_version != $bin_EDTA_raw_pl_version ]]; then + echo 'EDTA_raw.pl != bin/EDTA_raw.pl' + echo 'Please synchronize bin/EDTA_raw.pl with EDTA_raw.pl' + exit 1 +fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 0000000..03b6e41 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,20 @@ +name: linting +on: + pull_request: + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + + - name: Install pre-commit + run: pip install pre-commit + + - name: Run pre-commit + run: pre-commit run --all-files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..650f6a9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,11 @@ +repos: + - repo: local + hooks: + - id: check_binaries + name: Check binaries + language: system + entry: > + .github/check_binaries.sh + always_run: true + fail_fast: true + pass_filenames: false diff --git a/bin/EDTA_raw.pl b/bin/EDTA_raw.pl new file mode 100755 index 0000000..31c3cf0 --- /dev/null +++ b/bin/EDTA_raw.pl @@ -0,0 +1,761 @@ +#!/usr/bin/env perl +use warnings; +use strict; +use FindBin; +use File::Basename; +use File::Spec; # for obtaining the real path of a file +use Pod::Usage; + +######################################################## +##### Perform initial searches for TE candidates #### +##### Shujun Ou (shujun.ou.1@gmail.com, 07/16/2020) #### +######################################################## + +## Input: +# $genome + +## Output: +# $genome.LTR.raw.fa, $genome.LTR.intact.raw.fa, $genome.LTR.intact.raw.gff3 +# $genome.TIR.intact.fa, $genome.TIR.intact.raw.gff3 +# $genome.Helitron.intact.raw.fa, $genome.Helitron.intact.raw.gff3 +# $genome.LINE.raw.fa, $genome.SINE.raw.fa + +my $usage = "\nObtain raw TE libraries using various structure-based programs + +perl EDTA_raw.pl [options] + --genome [File] The genome FASTA + --species [rice|maize|others] Specify the species for identification + of TIR candidates. Default: others + --type [ltr|tir|helitron|line|sine|all] + Specify which type of raw TE candidates + you want to get. Default: all + --rmlib [FASTA] The RepeatModeler library, classified output. + --overwrite [0|1] If previous results are found, decide to + overwrite (1, rerun) or not (0, default). + --convert_seq_name [0|1] Convert long sequence name to <= 15 + characters and remove annotations (1, + default) or use the original (0) + --u [float] Neutral mutation rate to calculate the age of intact LTR elements. + Intact LTR age is found in this file: *EDTA_raw/LTR/*.pass.list. + Default: 1.3e-8 (per bp per year, from rice). + --genometools [path] Path to the GenomeTools program. (default: find from ENV) + --annosine [path] Path to the AnnoSINE program. (default: find from EDTA/bin) + --ltrretriever [path] Path to the LTR_retriever program. (default: find from ENV) + --blastplus [path] Path to the BLAST+ program. (default: find from ENV) + --tesorter [path] Path to the TEsorter program. (default: find from ENV) + --GRF [path] Path to the GRF program. (default: find from ENV) + --trf_path [path] Path to the TRF program. (default: find from ENV) + --mdust [path] Path to the mdust program. (default: find from ENV) + --repeatmasker [path] Path to the RepeatMasker program. (default: find from ENV) + --repeatmodeler [path] Path to the RepeatModeler2 program. (default: find from ENV) + --threads|-t [int] Number of theads to run this script. Default: 4 + --help|-h Display this help info +\n"; + +# pre-defined +my $genome = ''; +my $species = 'others'; +my $type = 'all'; +my $RMlib = 'null'; +my $overwrite = 0; #0, no rerun. 1, rerun even old results exist. +my $convert_name = 1; #0, use original seq names; 1 shorten names. +my $maxint = 5000; #maximum interval length (bp) between TIRs (for GRF in TIR-Learner) +my $miu = 1.3e-8; #mutation rate, per bp per year, from rice +my $threads = 4; +my $script_path = $FindBin::Bin; +my $cleanup_misclas = "$script_path/bin/cleanup_misclas.pl"; +my $get_range = "$script_path/bin/get_range.pl"; +my $rename_LTR = "$script_path/bin/rename_LTR_skim.pl"; +my $rename_RM = "$script_path/bin/rename_RM_TE.pl"; +my $filter_gff = "$script_path/bin/filter_gff3.pl"; +my $rename_tirlearner = "$script_path/bin/rename_tirlearner.pl"; +my $call_seq = "$script_path/bin/call_seq_by_list.pl"; +my $output_by_list = "$script_path/bin/output_by_list.pl"; +my $cleanup_tandem = "$script_path/bin/cleanup_tandem.pl"; +my $get_ext_seq = "$script_path/bin/get_ext_seq.pl"; +my $format_helitronscanner = "$script_path/bin/format_helitronscanner_out.pl"; +my $flank_filter = "$script_path/bin/flanking_filter.pl"; +my $make_bed = "$script_path/bin/make_bed_with_intact.pl"; +my $bed2gff = "$script_path/bin/bed2gff.pl"; +my $genometools = ''; #path to the genometools program +my $repeatmasker = ''; #path to the RepeatMasker program +my $repeatmodeler = ''; #path to the RepeatModeler program +my $LTR_retriever = ''; #path to the LTR_retriever program +my $TEsorter = ''; #path to the TEsorter program +my $blastplus = ''; #path to the blastn program +my $mdust = ''; #path to mdust +my $trf = ''; #path to trf +my $GRF = ''; #path to GRF +my $annosine = ""; #path to the AnnoSINE program + +# my $TIR_Learner = "$script_path/bin/TIR-Learner3/"; #tianyulu +# my $LTR_FINDER = "$script_path/bin/LTR_FINDER_parallel/LTR_FINDER_parallel"; #tianyulu +# my $LTR_HARVEST = "$script_path/bin/LTR_HARVEST_parallel/LTR_HARVEST_parallel"; #tianyulu +my $HelitronScanner_Runner = "$script_path/bin/run_helitron_scanner.sh"; + +my $TIR_Learner = ""; #path to TIR-Learner3 program #tianyulu +my $LTR_FINDER = ""; #path to LTR_FINDER_parallel program #tianyulu +my $LTR_HARVEST = ""; #path to LTR_HARVEST_parallel program #tianyulu +my $HelitronScanner = ""; #path to HelitronScanner program #tianyulu + +my $help = undef; + +# read parameters +my $k=0; +foreach (@ARGV){ + $genome = $ARGV[$k+1] if /^--genome$/i and $ARGV[$k+1] !~ /^-/; + $species = $ARGV[$k+1] if /^--species$/i and $ARGV[$k+1] !~ /^-/; + $type = lc $ARGV[$k+1] if /^--type$/i and $ARGV[$k+1] !~ /^-/; + $RMlib = $ARGV[$k+1] if /^--rmlib$/i and $ARGV[$k+1] !~ /^-/; + $overwrite = $ARGV[$k+1] if /^--overwrite$/i and $ARGV[$k+1] !~ /^-/; + $convert_name = $ARGV[$k+1] if /^--convert_seq_name$/i and $ARGV[$k+1] !~ /^-/; + $miu = $ARGV[$k+1] if /^--u$/i and $ARGV[$k+1] !~ /^-/; + $genometools = $ARGV[$k+1] if /^--genometools/i and $ARGV[$k+1] !~ /^-/; + $repeatmasker = $ARGV[$k+1] if /^--repeatmasker$/i and $ARGV[$k+1] !~ /^-/; + $repeatmodeler = $ARGV[$k+1] if /^--repeatmodeler$/i and $ARGV[$k+1] !~ /^-/; + $annosine = $ARGV[$k+1] if /^--annosine$/i and $ARGV[$k+1] !~ /^-/; + $LTR_retriever = $ARGV[$k+1] if /^--ltrretriever/i and $ARGV[$k+1] !~ /^-/; + $TEsorter = $ARGV[$k+1] if /^--tesorter$/i and $ARGV[$k+1] !~ /^-/; + $blastplus = $ARGV[$k+1] if /^--blastplus$/i and $ARGV[$k+1] !~ /^-/; + $mdust = $ARGV[$k+1] if /^--mdust$/i and $ARGV[$k+1] !~ /^-/; + $trf = $ARGV[$k+1] if /^--trf_path$/i and $ARGV[$k+1] !~ /^-/; + $GRF = $ARGV[$k+1] if /^--GRF$/i and $ARGV[$k+1] !~ /^-/; + $threads = $ARGV[$k+1] if /^--threads$|^-t$/i and $ARGV[$k+1] !~ /^-/; + $help = 1 if /^--help$|^-h$/i; + $k++; + } + +# check files and parameters +if ($help){ + pod2usage( { + -verbose => 0, + -exitval => 0, + -message => "$usage\n" } ); + } + +if (!-s $genome){ + pod2usage( { + -message => "At least 1 parameter is required:\n1) Input fasta file: --genome\n". + "\n$usage\n\n", + -verbose => 0, + -exitval => 2 } ); + } + +if ($species){ + $species =~ s/rice/Rice/i; + $species =~ s/maize/Maize/i; + $species =~ s/others/others/i; + die "The expected value for the species parameter is Rice or Maize or others!\n" unless $species eq "Rice" or $species eq "Maize" or $species eq "others"; + } + +die "The expected value for the type parameter is ltr or tir or helitron or all!\n" unless $type eq "ltr" or $type eq "line" or $type eq "tir" or $type eq "helitron" or $type eq "sine" or $type eq "all"; + +# check bolean +if ($overwrite != 0 and $overwrite != 1){ die "The expected value for the overwrite parameter is 0 or 1!\n"}; +if ($convert_name != 0 and $convert_name != 1){ die "The expected value for the convert_seq_name parameter is 0 or 1!\n"}; +if ($threads !~ /^[0-9]+$/){ die "The expected value for the threads parameter is an integer!\n"}; +if ($miu !~ /[0-9\.e\-]+/){ die "The expected value for the u parameter is float value without units!\n"} + +chomp (my $date = `date`); +print STDERR "$date\tEDTA_raw: Check dependencies, prepare working directories.\n\n"; + +# check files and dependencies +# die "The LTR_FINDER_parallel is not found in $LTR_FINDER!\n" unless -s $LTR_FINDER; #tianyulu +# die "The LTR_HARVEST_parallel is not found in $LTR_HARVEST!\n" unless -s $LTR_HARVEST; #tianyulu +# die "The TIR_Learner is not found in $TIR_Learner!\n" unless -s "$TIR_Learner/bin/main.py"; #tianyulu +die "The script get_range.pl is not found in $get_range!\n" unless -s $get_range; +die "The script rename_LTR_skim.pl is not found in $rename_LTR!\n" unless -s $rename_LTR; +die "The script filter_gff3.pl is not found in $filter_gff!\n" unless -s $filter_gff; +die "The script call_seq_by_list.pl is not found in $call_seq!\n" unless -s $call_seq; +die "The script output_by_list.pl is not found in $output_by_list!\n" unless -s $output_by_list; +die "The script rename_tirlearner.pl is not found in $rename_tirlearner!\n" unless -s $rename_tirlearner; +die "The script cleanup_tandem.pl is not found in $cleanup_tandem!\n" unless -s $cleanup_tandem; +die "The script get_ext_seq.pl is not found in $get_ext_seq!\n" unless -s $get_ext_seq; +# die "The HelitronScanner is not found in $HelitronScanner!\n" unless -s $HelitronScanner; #tianyulu +die "The script format_helitronscanner_out.pl is not found in $format_helitronscanner!\n" unless -s $format_helitronscanner; +die "The script flanking_filter.pl is not found in $flank_filter!\n" unless -s $flank_filter; +die "The script bed2gff.pl is not found in $bed2gff!\n" unless -s $bed2gff; +die "The script make_bed_with_intact.pl is not found in $make_bed!\n" unless -s $make_bed; + +# GenomeTools +chomp ($genometools=`command -v gt 2>/dev/null`) if $genometools eq ''; +$genometools =~ s/\s+$//; +$genometools = dirname($genometools) unless -d $genometools; +$genometools="$genometools/" if $genometools ne '' and $genometools !~ /\/$/; +die "Error: gt is not found in the genometools path $genometools!\n" unless -X "${genometools}gt"; +# RepeatMasker +my $rand=int(rand(1000000)); +chomp ($repeatmasker=`command -v RepeatMasker 2>/dev/null`) if $repeatmasker eq ''; +$repeatmasker =~ s/\s+$//; +$repeatmasker = dirname($repeatmasker) unless -d $repeatmasker; +$repeatmasker="$repeatmasker/" if $repeatmasker ne '' and $repeatmasker !~ /\/$/; +die "Error: RepeatMasker is not found in the RepeatMasker path $repeatmasker!\n" unless -X "${repeatmasker}RepeatMasker"; +# `cp $script_path/database/dummy060817.fa ./dummy060817.fa.$rand`; +`cp \"$script_path/database/dummy060817.fa\" ./dummy060817.fa.$rand`; #tianyulu +my $RM_test=`${repeatmasker}RepeatMasker -e ncbi -q -pa 1 -no_is -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand 2>/dev/null`; +die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/done//gi; +`rm dummy060817.fa.$rand*`; +# RepeatModeler +chomp ($repeatmodeler=`command -v RepeatModeler 2>/dev/null`) if $repeatmodeler eq ''; +$repeatmodeler =~ s/\s+$//; +$repeatmodeler = dirname($repeatmodeler) unless -d $repeatmodeler; +$repeatmodeler="$repeatmodeler/" if $repeatmodeler ne '' and $repeatmodeler !~ /\/$/; +die "Error: RepeatModeler is not found in the RepeatModeler path $repeatmodeler!\n" unless -X "${repeatmodeler}RepeatModeler"; +# AnnoSINE +chomp ($annosine=`command -v AnnoSINE_v2 2>/dev/null`) if $annosine eq ''; +$annosine =~ s/\s+$//; +$annosine = dirname($annosine) unless -d $annosine; +$annosine="$annosine/" if $annosine ne '' and $annosine !~ /\/$/; +die "Error: AnnoSINE is not found in the AnnoSINE path $annosine!\n" unless (-X "${annosine}AnnoSINE_v2"); +# LTR_retriever +chomp ($LTR_retriever=`command -v LTR_retriever 2>/dev/null`) if $LTR_retriever eq ''; +$LTR_retriever =~ s/\s+$//; +$LTR_retriever = dirname($LTR_retriever) unless -d $LTR_retriever; +$LTR_retriever="$LTR_retriever/" if $LTR_retriever ne '' and $LTR_retriever !~ /\/$/; +die "Error: LTR_retriever is not found in the LTR_retriever path $LTR_retriever!\n" unless -X "${LTR_retriever}LTR_retriever"; +# TEsorter +chomp ($TEsorter=`command -v TEsorter 2>/dev/null`) if $TEsorter eq ''; +$TEsorter =~ s/\s+$//; +$TEsorter = dirname($TEsorter) unless -d $TEsorter; +$TEsorter="$TEsorter/" if $TEsorter ne '' and $TEsorter !~ /\/$/; +die "Error: TEsorter is not found in the TEsorter path $TEsorter!\n" unless -X "${TEsorter}TEsorter"; +# makeblastdb, blastn +chomp ($blastplus=`command -v makeblastdb 2>/dev/null`) if $blastplus eq ''; +$blastplus =~ s/\s+$//; +$blastplus = dirname($blastplus) unless -d $blastplus; +$blastplus="$blastplus/" if $blastplus ne '' and $blastplus !~ /\/$/; +die "Error: makeblastdb is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}makeblastdb"; +die "Error: blastn is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}blastn"; +# mdust +chomp ($mdust=`command -v mdust 2>/dev/null`) if $mdust eq ''; +$mdust =~ s/\s+$//; +$mdust = dirname($mdust) unless -d $mdust; +$mdust = "$mdust/" if $mdust ne '' and $mdust !~ /\/$/; +die "Error: mdust is not found in the mdust path $mdust!\n" unless -X "${mdust}mdust"; +# trf +chomp ($trf=`command -v trf 2>/dev/null`) if $trf eq ''; +$trf=~s/\n$//; +`$trf 2>/dev/null`; +die "Error: Tandem Repeat Finder is not found in the TRF path $trf!\n" if $?==32256; +# GRF +chomp ($GRF = `command -v grf-main 2>/dev/null`) if $GRF eq ''; +$GRF =~ s/\n$//; +my $grfp= dirname ($GRF); +$grfp =~ s/\n$//; +`${grfp}grf-main 2>/dev/null`; +die "Error: The Generic Repeat Finder (GRF) is not found in the GRF path: $grfp\n" if $?==32256; + +# # TIR-Learner3 +# chomp ($TIR_Learner = `which TIR-Learner 2>/dev/null`) if $TIR_Learner eq ''; +# $TIR_Learner =~ s/\n$//; +# my $tirp= dirname ($TIR_Learner); +# $tirp =~ s/\n$//; +# `${tirp}TIR-Learner 2>/dev/null`; +# die "Error: TIR-Learner3 is not found in the TIR-Learner path: $tirp\n" if $?==32256; + +# TIR-Learner #tianyuLu +# Remove any trailing whitespace +$TIR_Learner =~ s/\s+$//; +if ($TIR_Learner eq "") { + # Find TIR-Learner path and remove any trailing newline + chomp ($TIR_Learner=`command -v TIR-Learner 2>/dev/null`); + die "Error: TIR-Learner not installed!\n" if $TIR_Learner eq ""; + # $TIR_Learner =~ s/\s+$//; +} else { + # # Extract directory name from path if path is not a directory + # $TIR_Learner = dirname($TIR_Learner) unless -d $TIR_Learner; + # If path is directory + if (-d $TIR_Learner) { + # # Add trailing slash if path not empty string and not already end with slash + # $TIR_Learner .= "/" if $TIR_Learner ne "" and $TIR_Learner !~ /\/$/; + # Add trailing slash if path not already end with slash + $TIR_Learner .= "/" if $TIR_Learner !~ /\/$/; + $TIR_Learner = "python3 $TIR_Learner/TIR-Learner.py"; + } +} +`$TIR_Learner 2>/dev/null`; +die "Error: TIR-Learner is not found in the path $TIR_Learner!\n" if $?==32256 || $?==2; + +# LTR_FINDER_parallel #tianyuLu +$LTR_FINDER =~ s/\s+$//; +if ($LTR_FINDER eq "") { + chomp ($LTR_FINDER=`command -v LTR_FINDER_parallel 2>/dev/null`); + die "Error: LTR_FINDER_parallel not installed!\n" if $LTR_FINDER eq ""; +} else { + if (-d $LTR_FINDER) { + $LTR_FINDER .= "/" if $LTR_FINDER !~ /\/$/; + $LTR_FINDER = "perl $LTR_FINDER/LTR_FINDER_parallel"; + } +} +`$LTR_FINDER 2>/dev/null`; +die "Error: LTR_FINDER_parallel is not found in the path $LTR_FINDER!\n" if $?==32256 || $?==2; + +# LTR_HARVEST_parallel #tianyuLu +$LTR_HARVEST =~ s/\s+$//; +if ($LTR_HARVEST eq "") { + chomp ($LTR_HARVEST=`command -v LTR_HARVEST_parallel 2>/dev/null`); + die "Error: LTR_HARVEST_parallel not installed!\n" if $LTR_HARVEST eq ""; +} else { + if (-d $LTR_HARVEST) { + $LTR_HARVEST .= "/" if $LTR_HARVEST !~ /\/$/; + $LTR_HARVEST = "perl $LTR_HARVEST/LTR_HARVEST_parallel"; + } +} +`$LTR_HARVEST 2>/dev/null`; +die "Error: LTR_HARVEST_parallel is not found in the path $LTR_HARVEST!\n" if $?==32256 || $?==2; + +# HelitronScanner #tianyuLu +$HelitronScanner =~ s/\s+$//; +if ($HelitronScanner eq "") { + chomp ($HelitronScanner=`command -v HelitronScanner 2>/dev/null`); + die "Error: HelitronScanner not installed!\n" if $HelitronScanner eq ""; +} else { + if (-d $HelitronScanner) { + $HelitronScanner .= "/" if $HelitronScanner !~ /\/$/; + } +} + +# make a softlink to the genome +my $genome_file = basename($genome); +`ln -s $genome $genome_file` unless -e $genome_file; +$genome = $genome_file; + +# check $RMlib +if ($RMlib ne 'null'){ + if (-e $RMlib){ + print "\tA RepeatModeler library $RMlib is provided via --rmlib. Please make sure this is a RepeatModeler2 generated and classified library (some levels of unknown classification is OK).\n\n"; + chomp ($RMlib = `realpath $RMlib`); + `ln -s $RMlib $genome.RM2.raw.fa` unless -s "$genome.RM2.raw.fa"; + $RMlib = "$genome.RM2.raw.fa"; + } else { + die "\tERROR: The RepeatModeler library $RMlib you specified is not found!\n\n"; + } + } + +# check if duplicated sequences found +my $id_mode = 0; #record the mode of id conversion. +my $id_len = `grep \\> $genome|perl -ne 'chomp; s/>//g; my \$len=length \$_; \$max=\$len if \$max<\$len; print "\$max\\n"'`; #find out the longest sequence ID length in the genome +$id_len =~ s/\s+$//; +$id_len = (split /\s+/, $id_len)[-1]; +my $raw_id = `grep \\> $genome|wc -l`; +my $old_id = `grep \\> $genome|sort -u|wc -l`; +if ($raw_id > $old_id){ + chomp ($date = `date`); + die "$date\tERROR: Identical sequence IDs found in the provided genome! Please resolve this issue and try again.\n"; + } + +if ($convert_name == 1){ +if (-s "$genome.mod"){ + $genome = "$genome.mod"; + } else { + +# remove sequence annotations (content after the first space in sequence names) and replace special characters with _, convert non-ATGC bases into Ns +`perl -nle 'my \$info=(split)[0]; \$info=~s/[\\~!@#\\\$%\\^&\\*\\(\\)\\+\\\-\\=\\?\\[\\]\\{\\}\\:;",\\<\\/\\\\\|]+/_/g; \$info=~s/_+/_/g; \$info=~s/[^ATGCN]/N/gi unless /^>/; print \$info' $genome > $genome.$rand.mod`; + +# try to shortern sequences +my $id_len_max = 13; # allowed longest length of a sequence ID in the input file +if ($id_len > $id_len_max){ + chomp ($date = `date`); + print "$date\tThe longest sequence ID in the genome contains $id_len characters, which is longer than the limit ($id_len_max)\n"; + print "\tTrying to reformat seq IDs...\n\t\tAttempt 1...\n"; + `perl -lne 'chomp; if (s/^>+//) {s/^\\s+//; \$_=(split)[0]; s/(.{1,$id_len_max}).*/>\$1/g;} print "\$_"' $genome.$rand.mod > $genome.$rand.temp`; + my $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + chomp ($date = `date`); + if ($old_id == $new_id){ + $id_mode = 1; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + print "\t\tAttempt 2...\n"; + `perl -ne 'chomp; if (/^>/) {\$_=">\$1" if /([0-9]+)/;} print "\$_\n"' $genome.$rand.mod > $genome.$rand.temp`; + $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + if ($old_id == $new_id){ + $id_mode = 2; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + `rm $genome.$rand.temp $genome.$rand.mod 2>/dev/null`; + die "$date\tERROR: Fail to convert seq IDs to <= $id_len_max characters! Please provide a genome with shorter seq IDs.\n\n"; + } + } + } else { + `mv $genome.$rand.mod $genome.mod`; + } +$genome = "$genome.mod"; +} +} + +# Make working directories +`mkdir $genome.EDTA.raw` unless -e "$genome.EDTA.raw" && -d "$genome.EDTA.raw"; +`mkdir $genome.EDTA.raw/LTR` unless -e "$genome.EDTA.raw/LTR" && -d "$genome.EDTA.raw/LTR"; +`mkdir $genome.EDTA.raw/SINE` unless -e "$genome.EDTA.raw/SINE" && -d "$genome.EDTA.raw/SINE"; +`mkdir $genome.EDTA.raw/LINE` unless -e "$genome.EDTA.raw/LINE" && -d "$genome.EDTA.raw/LINE"; +`mkdir $genome.EDTA.raw/TIR` unless -e "$genome.EDTA.raw/TIR" && -d "$genome.EDTA.raw/TIR"; +`mkdir $genome.EDTA.raw/Helitron` unless -e "$genome.EDTA.raw/Helitron" && -d "$genome.EDTA.raw/Helitron"; + + +########################### +###### LTR_retriever ###### +########################### + +if ($type eq "ltr" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find LTR candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/LTR"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and -s "$genome.LTR.raw.fa"){ + print STDERR "$date\tExisting result file $genome.LTR.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify LTR retrotransposon candidates from scratch.\n\n"; + +# run LTRharvest +if ($overwrite eq 0 and -s "$genome.harvest.combine.scn"){ + print STDERR "$date\tExisting raw result $genome.harvest.scn found!\n\t\tWill use this for further analyses.\n\n"; + } else { + # `perl $LTR_HARVEST -seq $genome -threads $threads -gt $genometools -size 1000000 -time 300`; + `$LTR_HARVEST -seq $genome -threads $threads -gt $genometools -size 1000000 -time 300`; #tianyulu + } + +# run LTR_FINDER_parallel +if ($overwrite eq 0 and -s "$genome.finder.combine.scn"){ + print STDERR "$date\tExisting raw result $genome.finder.combine.scn found!\n\t\tWill use this for further analyses.\n\n"; + } else { + # `perl $LTR_FINDER -seq $genome -threads $threads -harvest_out -size 1000000 -time 300`; + `$LTR_FINDER -seq $genome -threads $threads -harvest_out -size 1000000 -time 300`; #tianyulu + } + +# run LTR_retriever +if ($overwrite eq 0 and -s "$genome.LTRlib.fa"){ + print STDERR "$date\tExisting LTR_retriever result $genome.LTRlib.fa found!\n\t\tWill use this for further analyses.\n\n"; + } else { + `cat $genome.harvest.combine.scn $genome.finder.combine.scn > $genome.rawLTR.scn`; + `${LTR_retriever}LTR_retriever -genome $genome -inharvest $genome.rawLTR.scn -u $miu -threads $threads -noanno -trf_path $trf -blastplus $blastplus -repeatmasker $repeatmasker`; + } + +# get full-length LTR from pass.list +`awk '{if (\$1 !~ /#/) print \$1"\\t"\$1}' $genome.pass.list | perl $call_seq - -C $genome > $genome.LTR.intact.fa.ori`; +`perl -i -nle 's/\\|.*//; print \$_' $genome.LTR.intact.fa.ori`; +`perl $rename_LTR $genome.LTR.intact.fa.ori $genome.defalse > $genome.LTR.intact.fa.anno`; +`mv $genome.LTR.intact.fa.anno $genome.LTR.intact.fa.ori`; + +# remove simple repeats and candidates with simple repeats at terminals +`${mdust}mdust $genome.LTR.intact.fa.ori > $genome.LTR.intact.fa.ori.dusted`; +`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 100 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.LTR.intact.fa.ori.dusted > $genome.LTR.intact.fa.ori.dusted.cln`; + +# annotate and remove not LTR candidates +`${TEsorter}TEsorter $genome.LTR.intact.fa.ori.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; +`perl $cleanup_misclas $genome.LTR.intact.fa.ori.dusted.cln.rexdb.cls.tsv`; +`mv $genome.LTR.intact.fa.ori.dusted.cln.cln $genome.LTR.intact.raw.fa`; +`mv $genome.LTR.intact.fa.ori.dusted.cln.cln.list $genome.LTR.intact.raw.fa.anno.list`; +`cp $genome.LTR.intact.raw.fa.anno.list ../`; + +# generate annotated output and gff +`perl $output_by_list 1 $genome.LTR.intact.fa.ori 1 $genome.LTR.intact.raw.fa -FA -ex|grep \\>|perl -nle 's/>//; print "Name\\t\$_"' > $genome.LTR.intact.fa.ori.rmlist`; +`perl $filter_gff $genome.pass.list.gff3 $genome.LTR.intact.fa.ori.rmlist | perl -nle 's/LTR_retriever/EDTA/gi; print \$_' > $genome.LTR.intact.raw.gff3`; +`rm $genome`; + } + +# copy result files out +`touch $genome.LTRlib.fa` unless -e "$genome.LTRlib.fa"; +`cp $genome.LTRlib.fa $genome.LTR.raw.fa`; +`cp $genome.LTRlib.fa ../$genome.LTR.raw.fa`; +`cp $genome.LTR.intact.raw.fa $genome.LTR.intact.raw.gff3 ../ 2>/dev/null`; +`cp $genome.LTR.intact.fa ../$genome.LTR.intact.raw.fa` if -s "$genome.LTR.intact.fa"; +`cp $genome.LTR.intact.gff3 ../$genome.LTR.intact.raw.gff3` if -s "$genome.LTR.intact.gff3"; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: LTR results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.LTR.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.LTR.raw.fa"){ + print STDERR "$date\tFinish finding LTR candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The LTR result file has 0 bp!\n\n"; + } + +} + + +############################# +###### AnnoSINE ###### +############################# +if ($type eq "sine" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find SINE candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/SINE"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Remove existing results +`rm -rf Seed_SINE.fa Step* HMM_out 2>/dev/null` if $overwrite eq 1; + +# run AnnoSINE_v2 +my $status; # record status of AnnoSINE execution +if (-s "Seed_SINE.fa"){ + print STDERR "$date\tExisting result file Seed_SINE.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun AnnoSINE_v2.\n\n"; + } else { + $status = system("python3 ${annosine}AnnoSINE_v2 -t $threads -a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1 3 $genome ./ > /dev/null 2>&1"); + } + +# filter and reclassify AnnoSINE candidates with TEsorter and make SINE library +if (-s "Seed_SINE.fa"){ + # annotate and remove non-SINE candidates + `awk '{gsub(/Unknown/, "unknown"); print \$1}' Seed_SINE.fa > $genome.AnnoSINE.raw.fa`; + `${TEsorter}TEsorter $genome.AnnoSINE.raw.fa --disable-pass2 -p $threads 2>/dev/null`; + `touch $genome.AnnoSINE.raw.fa.rexdb.cls.tsv` unless -e "$genome.AnnoSINE.raw.fa.rexdb.cls.tsv"; + `perl $cleanup_misclas $genome.AnnoSINE.raw.fa.rexdb.cls.tsv`; + + # clean up tandem repeat + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.AnnoSINE.raw.fa.cln > $genome.SINE.raw.fa`; + } +elsif ($status == 0) { + print "\t\tAnnoSINE is finished without error, but the Seed_SINE.fa file is not produced.\n\n"; + `touch $genome.SINE.raw.fa`; + } +else { + print "\t\tAnnoSINE exited with error, please test run AnnoSINE to make sure it's working.\n\n"; + } + +# copy result files out +`cp $genome.SINE.raw.fa ../`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: SINE results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.SINE.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.SINE.raw.fa"){ + print STDERR "$date\tFinish finding SINE candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The SINE result file has 0 bp!\n\n"; + } + +} + + +############################# +###### RepeatModeler ###### +############################# + +if ($type eq "line" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find LINE candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/LINE"; +`ln -s ../../$genome $genome` unless -s $genome; +`cp ../../$RMlib $RMlib` if $RMlib ne 'null'; + +# Try to recover existing results or run RepeatModeler2 +chomp ($date = `date`); +if ($overwrite eq 0 and -s $RMlib){ + if (-s "$genome-families.fa"){ + print STDERR "$date\tExisting result file $genome-families.fa found!\n\t\tWill not use the provided RepeatModeler2 library since --overwrite 0.\n\t\tPlease specify --overwrite 1 if you want to use the provided --rmlib file.\n\n"; + } else { + `cp $RMlib "$genome-families.fa" 2>/dev/null`; + } + } + +if ($overwrite eq 0 and -s "$genome-families.fa"){ + print STDERR "$date\tExisting result file $genome-families.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + # run RepeatModeler2 + print STDERR "$date\tIdentify LINE retrotransposon candidates from scratch.\n\n"; + my $status; # record status of RepeatModeler execution + `${repeatmodeler}BuildDatabase -name $genome $genome`; + $status = system("${repeatmodeler}RepeatModeler -engine ncbi -threads $threads -database $genome > repeatmodeler.log 2>&1"); + if ($status != 0) { + # Execute the old version of RepeatModeler + $status = system("${repeatmodeler}RepeatModeler -engine ncbi -pa $threads -database $genome > repeatmodeler.log 2>&1"); + print "ERROR: RepeatModeler did not run correctly. Please test run this command: + ${repeatmodeler}RepeatModeler -engine ncbi -pa $threads -database $genome + " and exit unless $status == 0; + } + `rm $genome.nhr $genome.nin $genome.nnd $genome.nni $genome.nog $genome.nsq $genome.njs $genome.translation 2>/dev/null`; + } + +# filter and reclassify RepeatModeler candidates with TEsorter and make LINE library +if (-s "$genome-families.fa"){ + # annotate and remove misclassified candidates + `awk '{gsub(/Unknown/, "unknown"); print \$1}' $genome-families.fa > $genome.RM2.raw.fa` if -e "$genome-families.fa"; + `${TEsorter}TEsorter $genome.RM2.raw.fa --disable-pass2 -p $threads 2>/dev/null`; + `perl $cleanup_misclas $genome.RM2.raw.fa.rexdb.cls.tsv`; + + # reclassify clean candidates + `${TEsorter}TEsorter $genome.RM2.raw.fa.cln --disable-pass2 -p $threads 2>/dev/null`; + `perl -nle 's/>\\S+\\s+/>/; print \$_' $genome.RM2.raw.fa.cln.rexdb.cls.lib > $genome.RM2.raw.fa.cln`; + + # clean up tandem repeat + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.RM2.raw.fa.cln > $genome.RM2.raw.fa.cln2`; + `grep -P 'LINE|SINE' $genome.RM2.raw.fa.cln2 | perl $output_by_list 1 $genome.RM2.raw.fa.cln2 1 - -FA > $genome.LINE.raw.fa`; + `grep -P 'LINE|SINE' $genome.RM2.raw.fa.cln2 | perl $output_by_list 1 $genome.RM2.raw.fa.cln2 1 - -FA -ex > $genome.RM2.fa`; + } else { + print "\t\tRepeatModeler is finished, but the $genome-families.fa file is not produced.\n\n"; + `touch $genome.RM2.raw.fa $genome.LINE.raw.fa $genome.RM2.fa`; + } + +# copy result files out +`cp $genome.LINE.raw.fa $genome.RM2.fa ../`; #update the filtered RM2 result in the EDTA/raw folder +`cp $genome.RM2.raw.fa ../../`; #update the raw RM2 result in the EDTA folder +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: LINE results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.LINE.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.LINE.raw.fa"){ + print STDERR "$date\tFinish finding LINE candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The LINE result file has 0 bp!\n\n"; + } +} + + +########################### +###### TIR-Learner ###### +########################### + +if ($type eq "tir" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find TIR candidates.\n\n"; + +# pre-set parameters +my $genome_file_real_path=File::Spec->rel2abs($genome); # the genome file with real path + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/TIR"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and (-s "$genome.TIR.intact.raw.fa" or -s "$genome.TIR.intact.fa")){ + print STDERR "$date\tExisting result file $genome.TIR.intact.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify TIR candidates from scratch.\n\n"; + print STDERR "Species: $species\n"; + + # run TIR-Learner + if ($overwrite eq 0 and -s "./TIR-Learner-Result/TIR-Learner_FinalAnn.fa"){ + print STDERR "$date\tExisting raw result TIR-Learner_FinalAnn.fa found!\n\t\tWill use this for further analyses.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + `$TIR_Learner -f $genome_file_real_path -s $species -t $threads -l $maxint -c -o $genome_file_real_path.EDTA.raw/TIR --grf_path $grfp --gt_path $genometools`; #TianyuLu + } + + # clean raw predictions with flanking alignment + `perl $rename_tirlearner ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa | perl -nle 's/TIR-Learner_//g; print \$_' > $genome.TIR`; + `perl $get_ext_seq $genome $genome.TIR`; + `perl $flank_filter -genome $genome -query $genome.TIR.ext30.fa -miniden 90 -mincov 0.9 -maxct 20 -blastplus $blastplus -t $threads`; + + # recover superfamily info + `perl $output_by_list 1 $genome.TIR 1 $genome.TIR.ext30.fa.pass.fa -FA -MSU0 -MSU1 > $genome.TIR.ext30.fa.pass.fa.ori`; + + # remove simple repeats and candidates with simple repeats at terminals + `${mdust}mdust $genome.TIR.ext30.fa.pass.fa.ori > $genome.TIR.ext30.fa.pass.fa.dusted`; + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.TIR.ext30.fa.pass.fa.dusted > $genome.TIR.ext30.fa.pass.fa.dusted.cln`; + + # annotate and remove non-TIR candidates + `${TEsorter}TEsorter $genome.TIR.ext30.fa.pass.fa.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; + `perl $cleanup_misclas $genome.TIR.ext30.fa.pass.fa.dusted.cln.rexdb.cls.tsv`; + `mv $genome.TIR.ext30.fa.pass.fa.dusted.cln.cln $genome.TIR.intact.raw.fa`; + `cp $genome.TIR.ext30.fa.pass.fa.dusted.cln.cln.list $genome.TIR.intact.raw.fa.anno.list`; + `cp $genome.TIR.intact.raw.fa.anno.list ../`; + + # get gff3 of intact TIR elements + `perl -nle 's/\\-\\+\\-/_Len:/; my (\$chr, \$method, \$supfam, \$s, \$e, \$anno) = (split)[0,1,2,3,4,8]; my \$class='DNA'; \$class='MITE' if \$e-\$s+1 <= 600; my (\$tir, \$iden, \$tsd)=(\$1, \$2/100, \$3) if \$anno=~/TIR:(.*)_([0-9.]+)_TSD:([a-z0-9._]+)_LEN/i; print "\$chr \$s \$e \$chr:\$s..\$e \$class/\$supfam structural \$iden . . . TSD=\$tsd;TIR=\$tir"' ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3 | perl $output_by_list 4 - 1 $genome.TIR.intact.raw.fa -MSU0 -MSU1 > $genome.TIR.intact.raw.bed`; + `perl $bed2gff $genome.TIR.intact.raw.bed TIR > $genome.TIR.intact.raw.gff3`; + } + +# copy result files out +`cp $genome.TIR.intact.bed ../$genome.TIR.intact.raw.bed` if -s "$genome.TIR.intact.bed"; # recover /dev/null`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: TIR results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.TIR.intact.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.TIR.intact.raw.fa"){ + print STDERR "$date\tFinish finding TIR candidates.\n\n"; + } else { + print STDERR "Warning: The TIR result file has 0 bp!\n\n"; + } + +} + + +############################# +###### HelitronScanner ###### +############################# + +if ($type eq "helitron" or $type eq "all"){ + +chomp ($date = `date`); +print STDERR "$date\tStart to find Helitron candidates.\n\n"; + +# enter the working directory and create genome softlink +chdir "$genome.EDTA.raw/Helitron"; +`ln -s ../../$genome $genome` unless -s $genome; + +# Try to recover existing results +chomp ($date = `date`); +if ($overwrite eq 0 and (-s "$genome.Helitron.intact.raw.fa" or -s "$genome.Helitron.intact.fa")){ + print STDERR "$date\tExisting result file $genome.Helitron.intact.raw.fa found!\n\t\tWill keep this file without rerunning this module.\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + print STDERR "$date\tIdentify Helitron candidates from scratch.\n\n"; + +# run HelitronScanner +`$HelitronScanner_Runner $genome $threads \"$HelitronScanner\"`; + +# filter candidates based on repeatness of flanking regions +`perl $format_helitronscanner -genome $genome -sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1`; +`perl $flank_filter -genome $genome -query $genome.HelitronScanner.filtered.ext.fa -miniden 90 -mincov 0.9 -maxct 5 -blastplus $blastplus -t $threads`; #more relaxed +#`perl $flank_filter -genome $genome -query $genome.HelitronScanner.filtered.ext.fa -miniden 80 -mincov 0.8 -maxct 5 -blastplus $blastplus -t $threads`; #more stringent + +# remove simple repeats and candidates with simple repeats at terminals +`perl $output_by_list 1 $genome.HelitronScanner.filtered.fa 1 $genome.HelitronScanner.filtered.ext.fa.pass.fa -FA > $genome.HelitronScanner.filtered.fa.pass.fa`; +`${mdust}mdust $genome.HelitronScanner.filtered.fa.pass.fa > $genome.HelitronScanner.filtered.fa.pass.fa.dusted`; +`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 100 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.HelitronScanner.filtered.fa.pass.fa.dusted | perl -nle 's/^(>.*)\\s+(.*)\$/\$1#DNA\\/Helitron\\t\$2/; print \$_' > $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln`; + +# annotate and remove non-Helitron candidates +`${TEsorter}TEsorter $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln --disable-pass2 -p $threads 2>/dev/null`; +`perl $cleanup_misclas $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.rexdb.cls.tsv`; +`mv $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln $genome.Helitron.intact.raw.fa`; +`cp $genome.HelitronScanner.filtered.fa.pass.fa.dusted.cln.cln.list $genome.Helitron.intact.raw.fa.anno.list`; +`cp $genome.Helitron.intact.raw.fa.anno.list ../`; + +# get intact Helitrons and gff3 +`perl $make_bed $genome.Helitron.intact.raw.fa > $genome.Helitron.intact.raw.bed`; +`perl $bed2gff $genome.Helitron.intact.raw.bed HEL > $genome.Helitron.intact.raw.gff3`; + } + +# copy result files out +`cp $genome.Helitron.intact.bed ../$genome.Helitron.intact.raw.bed` if -s "$genome.Helitron.intact.bed"; # recover /dev/null`; +chdir '../..'; + +# check results +chomp ($date = `date`); +die "Error: Helitron results not found!\n\n" unless -e "$genome.EDTA.raw/$genome.Helitron.intact.raw.fa"; +if (-s "$genome.EDTA.raw/$genome.Helitron.intact.raw.fa"){ + print STDERR "$date\tFinish finding Helitron candidates.\n\n"; + } else { + print STDERR "$date\tWarning: The Helitron result file has 0 bp!\n\n"; + } + +} + +chomp ($date = `date`); +print STDERR "$date\tExecution of EDTA_raw.pl is finished!\n\n"; diff --git a/bin/setup_LTR_retriever_postprocess.sh b/bin/setup_LTR_retriever_postprocess.sh new file mode 100755 index 0000000..140b4b5 --- /dev/null +++ b/bin/setup_LTR_retriever_postprocess.sh @@ -0,0 +1,26 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/LTR_retriever_postprocess.pl << EOF + +my \$genome = 'genome'; +my \$threads = $1; + +my \$call_seq = '$script_path/call_seq_by_list.pl'; +my \$rename_LTR = '$script_path/rename_LTR_skim.pl'; +my \$mdust = ''; # Assumed on PATH +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; +my \$trf = '$(which trf)'; +my \$TEsorter = ''; # Assumed on PATH +my \$cleanup_misclas= '$script_path/cleanup_misclas.pl'; +my \$output_by_list = '$script_path/output_by_list.pl'; +my \$filter_gff = '$script_path/filter_gff3.pl'; + +EOF + +sed -n 443,462p "$script_path/EDTA_raw.pl" \ + >> input/LTR_retriever_postprocess.pl + +sed -n 466,472p "$script_path/EDTA_raw.pl" \ + >> input/LTR_retriever_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index 918b569..c521005 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -42,5 +42,15 @@ process { withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' } + + withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/ltr" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/conf/test.config b/conf/test.config index e921133..e0a2931 100644 --- a/conf/test.config +++ b/conf/test.config @@ -7,5 +7,5 @@ process { } params { - genomes = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' + genomes = 'https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa' } \ No newline at end of file diff --git a/modules/local/ltr_retriever_postprocess/environment.yml b/modules/local/ltr_retriever_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/ltr_retriever_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf new file mode 100644 index 0000000..c957229 --- /dev/null +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -0,0 +1,80 @@ +process LTR_RETRIEVER_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/genome.pass.list" + path "input/genome.pass.list.gff3" + path "input/genome.defalse" + path "input/genome.LTRlib.fa" + + output: + tuple val(meta), path('*.LTR.raw.fa') , emit: raw_fa + tuple val(meta), path('*.LTR.intact.raw.fa') , emit: intact_raw_fa + tuple val(meta), path('*.LTR.intact.raw.gff3') , emit: intact_raw_gff3 + tuple val(meta), path('*.LTR.intact.raw.fa.anno.list') , emit: anno_list + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_LTR_retriever_postprocess.sh \\ + $task.cpus + + cd input + + perl LTR_retriever_postprocess.pl + + cd - + + mv \\ + genome.LTR.raw.fa \\ + ${prefix}.LTR.raw.fa + + mv \\ + genome.LTR.intact.raw.fa \\ + ${prefix}.genome.LTR.intact.raw.fa + + mv \\ + genome.LTR.intact.raw.gff3 \\ + ${prefix}.LTR.intact.raw.gff3 + + mv \\ + genome.LTR.intact.raw.fa.anno.list \\ + ${prefix}.LTR.intact.raw.fa.anno.list + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/nf-core/ltrretriever/ltrretriever/main.nf b/modules/nf-core/ltrretriever/ltrretriever/main.nf new file mode 100644 index 0000000..ca97232 --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/main.nf @@ -0,0 +1,96 @@ +process LTRRETRIEVER_LTRRETRIEVER { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ltr_retriever:2.9.9--hdfd78af_0': + 'biocontainers/ltr_retriever:2.9.9--hdfd78af_0' }" + + input: + tuple val(meta), path(genome) + path(harvest) + path(finder) + path(mgescan) + path(non_tgca) + + output: + tuple val(meta), path("*.log") , emit: log + tuple val(meta), path("${prefix}.pass.list"), emit: pass_list , optional: true + tuple val(meta), path("*.pass.list.gff3") , emit: pass_list_gff , optional: true + tuple val(meta), path("*.LTRlib.fa") , emit: ltrlib , optional: true + tuple val(meta), path("${prefix}.out") , emit: annotation_out , optional: true + tuple val(meta), path("*.out.gff3") , emit: annotation_gff , optional: true + tuple val(meta), path("*.defalse") , emit: defalse , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def inharvest = harvest ? "-inharvest $harvest" : '' + def infinder = finder ? "-infinder $finder" : '' + def inmgescan = mgescan ? "-inmgescan $mgescan" : '' + def non_tgca_file = non_tgca ? "-nonTGCA $non_tgca" : '' + def writable_genome = "${genome.baseName}.writable.${genome.extension}" + // writable_genome: + // This is needed to avoid LTR_retriever:2.9.9 failure when the input `genome` is + // readonly. LTR_retriever triggers a 'die' if the genome is readonly. + // See: https://github.com/oushujun/LTR_retriever/blob/4039eb7778fd9cbc60021e99a8693285e0fa2daf/LTR_retriever#L312 + // + // This copy with permissions logic can be removed once https://github.com/oushujun/LTR_retriever/issues/176 + // has been resolved. + """ + cp \\ + $genome \\ + $writable_genome + + chmod \\ + a+w \\ + $writable_genome + + LTR_retriever \\ + -genome $writable_genome \\ + $inharvest \\ + $infinder \\ + $inmgescan \\ + $non_tgca_file \\ + -threads $task.cpus \\ + $args \\ + &> >(tee "${prefix}.log" 2>&1) \\ + || echo "Errors from LTR_retriever printed to ${prefix}.log" + + mv "${writable_genome}.pass.list" "${prefix}.pass.list" || echo ".pass.list was not produced" + mv "${writable_genome}.pass.list.gff3" "${prefix}.pass.list.gff3" || echo ".pass.list.gff3 was not produced" + mv "${writable_genome}.LTRlib.fa" "${prefix}.LTRlib.fa" || echo ".LTRlib.fa was not produced" + mv "${writable_genome}.out" "${prefix}.out" || echo ".out was not produced" + mv "${writable_genome}.out.gff3" "${prefix}.out.gff3" || echo ".out.gff3 was not produced" + mv "${writable_genome}.defalse" "${prefix}.defalse" || echo ".defalse was not produced" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_retriever: \$(LTR_retriever -h 2>&1 | grep '### LTR_retriever' | sed 's/### LTR_retriever //; s/ ###//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def touch_out = args.contains('-noanno') ? '' : "touch ${prefix}.out" + def touch_out_gff = args.contains('-noanno') ? '' : "touch ${prefix}.out.gff3" + """ + touch "${prefix}.log" + touch "${prefix}.pass.list" + touch "${prefix}.pass.list.gff3" + touch "${prefix}.LTRlib.fa" + $touch_out + $touch_out_gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_retriever: \$(LTR_retriever -h 2>&1 | grep '### LTR_retriever' | sed 's/### LTR_retriever //; s/ ###//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap new file mode 100644 index 0000000..4942e1a --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test.snap @@ -0,0 +1,160 @@ +{ + "versions": { + "content": [ + "\"LTRRETRIEVER_LTRRETRIEVER\":\n LTR_retriever: v2.9.9\n" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-19T11:17:50.208819" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.pass.list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.pass.list.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.LTRlib.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.out.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + + ], + "7": [ + "versions.yml:md5,3ab159acaee06b342b56e2d35e5e669b" + ], + "annotation_gff": [ + [ + { + "id": "test" + }, + "test.out.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "annotation_out": [ + [ + { + "id": "test" + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "defalse": [ + + ], + "log": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ltrlib": [ + [ + { + "id": "test" + }, + "test.LTRlib.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pass_list": [ + [ + { + "id": "test" + }, + "test.pass.list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pass_list_gff": [ + [ + { + "id": "test" + }, + "test.pass.list.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3ab159acaee06b342b56e2d35e5e669b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-12-05T12:39:11.669541" + }, + "annotation_out": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.out:md5,33d89bea9031f25de8f0d3591ab94d87" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-16T14:18:02.458476" + }, + "versions_no_ltr": { + "content": [ + [ + "versions.yml:md5,3ab159acaee06b342b56e2d35e5e669b" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-16T14:03:52.324194" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index ccf5850..7eb1232 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,3 +1,7 @@ +params { + publish_dir_mode = 'copy' +} + process { cpus = { 1 * task.attempt } diff --git a/nf-test.config b/nf-test.config index c3a9a1e..29d7e09 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,7 +1,7 @@ config { testsDir "." workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" - configFile "test/nf-test/nextflow.config" + configFile "tests/nf-test/nextflow.config" plugins { load "nft-bam@0.4.0" diff --git a/test/Alyrata.test.fa b/tests/Alyrata.test.fa similarity index 100% rename from test/Alyrata.test.fa rename to tests/Alyrata.test.fa diff --git a/test/Col.test.fa b/tests/Col.test.fa similarity index 100% rename from test/Col.test.fa rename to tests/Col.test.fa diff --git a/test/Ler.test.fa b/tests/Ler.test.fa similarity index 100% rename from test/Ler.test.fa rename to tests/Ler.test.fa diff --git a/test/README.txt b/tests/README.txt similarity index 100% rename from test/README.txt rename to tests/README.txt diff --git a/test/genome.cds.fa b/tests/genome.cds.fa similarity index 100% rename from test/genome.cds.fa rename to tests/genome.cds.fa diff --git a/test/genome.cds.list b/tests/genome.cds.list similarity index 100% rename from test/genome.cds.list rename to tests/genome.cds.list diff --git a/test/genome.exclude.bed b/tests/genome.exclude.bed similarity index 100% rename from test/genome.exclude.bed rename to tests/genome.exclude.bed diff --git a/test/genome.fa b/tests/genome.fa similarity index 100% rename from test/genome.fa rename to tests/genome.fa diff --git a/test/nf-test/nextflow.config b/tests/nf-test/nextflow.config similarity index 100% rename from test/nf-test/nextflow.config rename to tests/nf-test/nextflow.config diff --git a/test/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test similarity index 50% rename from test/nf-test/small/main.nf.test rename to tests/nf-test/small/main.nf.test index 7d40a02..ce37a4f 100644 --- a/test/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -13,7 +13,28 @@ nextflow_pipeline { } then { - def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + + def stable_path = getAllFilesFromDir( + params.outdir, + false, + [ + 'pipeline_info/*.{html,json,txt,yml}', + 'ltr/*.pp.LTR.intact.raw.gff3', + 'ltr/*.pp.LTR.raw.fa', + ], + null, + ['**'] + ) + + def stable_name = getAllFilesFromDir( + params.outdir, + true, + [ + 'pipeline_info/*.{html,json,txt,yml}' + ], + null, + ['**'] + ) assertAll( { assert workflow.success}, @@ -21,7 +42,8 @@ nextflow_pipeline { [ 'successful tasks': workflow.trace.succeeded().size(), 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), - 'stable paths': stable_path + 'stable paths': stable_path, + 'stable names': getRelativePath(stable_name, outputDir), ] ).match() } ) diff --git a/test/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap similarity index 72% rename from test/nf-test/small/main.nf.test.snap rename to tests/nf-test/small/main.nf.test.snap index 5a164b2..a943b0a 100644 --- a/test/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 16, + "successful tasks": 17, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -42,6 +42,12 @@ "LTRRETRIEVER_LTRRETRIEVER": { "LTR_retriever": "v2.9.9" }, + "LTR_RETRIEVER_POSTPROCESS": { + "perl": "v5.32.1", + "trf": 4.09, + "TEsorter": "1.4.7", + "mdust": "2006.10.17" + }, "REPEATMODELER_BUILDDATABASE": { "repeatmodeler": "2.0.5" }, @@ -56,7 +62,16 @@ } }, "stable paths": [ - + "genome.pp.LTR.intact.raw.fa.anno.list:md5,51261f020350b448acdf89d8fb625448", + "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25" + ], + "stable names": [ + "ltr", + "ltr/genome.pp.LTR.intact.raw.fa.anno.list", + "ltr/genome.pp.LTR.intact.raw.gff3", + "ltr/genome.pp.LTR.raw.fa", + "ltr/genome.pp.genome.LTR.intact.raw.fa", + "pipeline_info" ] } ], @@ -64,6 +79,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-03T14:20:03.748125" + "timestamp": "2024-12-05T12:10:52.622584" } } \ No newline at end of file diff --git a/test/nf-test/tiny/main.nf.test b/tests/nf-test/tiny/main.nf.test similarity index 100% rename from test/nf-test/tiny/main.nf.test rename to tests/nf-test/tiny/main.nf.test diff --git a/test/nf-test/tiny/main.nf.test.snap b/tests/nf-test/tiny/main.nf.test.snap similarity index 100% rename from test/nf-test/tiny/main.nf.test.snap rename to tests/nf-test/tiny/main.nf.test.snap diff --git a/workflows/edta.nf b/workflows/edta.nf index 05a6da3..a4799cf 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -9,11 +9,14 @@ include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmod include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' +include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' workflow EDTA { + main: + // Versions channel ch_versions = Channel.empty() @@ -36,7 +39,6 @@ workflow EDTA { // MODULE: LTRHARVEST LTRHARVEST ( ch_sanitized_fasta ) - ch_ltrharvest_gff3 = LTRHARVEST.out.gff3 ch_ltrharvest_scn = LTRHARVEST.out.scn ch_versions = ch_versions.mix(LTRHARVEST.out.versions) @@ -44,7 +46,6 @@ workflow EDTA { // MODULE: LTRFINDER LTRFINDER { ch_sanitized_fasta } - ch_ltrfinder_gff3 = LTRFINDER.out.gff ch_ltrfinder_scn = LTRFINDER.out.scn ch_versions = ch_versions.mix(LTRFINDER.out.versions) @@ -62,17 +63,17 @@ workflow EDTA { ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) LTRRETRIEVER_LTRRETRIEVER ( - ch_ltrretriever_inputs.map { meta, fasta, ltr -> [ meta, fasta ] }, - ch_ltrretriever_inputs.map { meta, fasta, ltr -> ltr }, + ch_ltrretriever_inputs.map { meta, fasta, _ltr -> [ meta, fasta ] }, + ch_ltrretriever_inputs.map { _meta, _fasta, ltr -> ltr }, [], [], [] ) - ch_ltrretriever_log = LTRRETRIEVER_LTRRETRIEVER.out.log ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list - ch_annotation_out = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out + ch_pass_list_gff = LTRRETRIEVER_LTRRETRIEVER.out.pass_list_gff ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff + ch_defalse = LTRRETRIEVER_LTRRETRIEVER.out.defalse ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) @@ -102,7 +103,7 @@ workflow EDTA { def size = fasta.size() def size_threshold = 100_000 // bytes -> bp - // TODO: Not the best way to set a size threshould + // TODO: Not the best way to set a size threshold // but it is simple // This is needed to avoid, // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. @@ -151,6 +152,32 @@ workflow EDTA { ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) + // MODULE: LTR_RETRIEVER_POSTPROCESS + ltr_retriever_postprocess_inputs = ch_sanitized_fasta + | join(ch_pass_list) + | join(ch_pass_list_gff) + | join(ch_annotation_gff) + | join(ch_defalse) + | join(ch_ltrlib) + | multiMap { meta, fasta, pass, p_gff, a_gff, defalse, ltr -> + genome: [ meta, fasta ] + pass : pass + p_gff : p_gff + a_gff : a_gff + defalse : defalse + ltr : ltr + } + + LTR_RETRIEVER_POSTPROCESS ( + ltr_retriever_postprocess_inputs.genome, + ltr_retriever_postprocess_inputs.pass, + ltr_retriever_postprocess_inputs.p_gff, + ltr_retriever_postprocess_inputs.defalse, + ltr_retriever_postprocess_inputs.ltr, + ) + + ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) + // Function: Save versions ch_versions = ch_versions @@ -168,4 +195,7 @@ workflow EDTA { cache: false ) + emit: + versions_yml = ch_versions_yml // [ software_versions.yml ] + } \ No newline at end of file From 82b34ac8ad50c459a0842616d6fb44ca31955731 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 15:52:06 +1300 Subject: [PATCH 31/49] Fixed singularity container --- modules/local/ltr_retriever_postprocess/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf index c957229..e679be6 100644 --- a/modules/local/ltr_retriever_postprocess/main.nf +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -4,7 +4,7 @@ process LTR_RETRIEVER_POSTPROCESS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64d26063bedc2efcba20750a408a21f50907986d0d9aee685b03d7d05d3fbd8b/data': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" input: From c94149666446b326f40bdbdf1fbac42bbb1711f2 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 5 Dec 2024 16:22:50 +1300 Subject: [PATCH 32/49] Fixed nextflow-setup version --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 20d4b62..d53140c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -56,7 +56,7 @@ jobs: uses: actions/checkout@v4.2.1 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@v2.0.0 with: version: "${{ matrix.NXF_VER }}" From 9816823772de4041706a1deb20f9e23d7fd12f29 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 11 Dec 2024 14:31:17 +1300 Subject: [PATCH 33/49] Updated master from upstream --- bin/EDTA_raw.pl | 31 +-- bin/setup_LTR_retriever_postprocess.sh | 4 +- modules/gallvp/annosine/environment.yml | 6 + modules/gallvp/annosine/main.nf | 58 ++++++ modules/gallvp/annosine/meta.yml | 51 +++++ modules/gallvp/annosine/tests/main.nf.test | 61 ++++++ .../gallvp/annosine/tests/main.nf.test.snap | 72 +++++++ modules/gallvp/annosine/tests/nextflow.config | 5 + modules/gallvp/tirlearner/environment.yml | 5 + modules/gallvp/tirlearner/main.nf | 75 +++++++ modules/gallvp/tirlearner/meta.yml | 94 +++++++++ modules/gallvp/tirlearner/tests/main.nf.test | 91 +++++++++ .../gallvp/tirlearner/tests/main.nf.test.snap | 155 ++++++++++++++ modules/local/sanitize/main.nf | 38 ++++ modules/nf-core/cat/cat/environment.yml | 5 + modules/nf-core/cat/cat/main.nf | 78 +++++++ modules/nf-core/cat/cat/meta.yml | 43 ++++ modules/nf-core/cat/cat/tests/main.nf.test | 191 ++++++++++++++++++ .../nf-core/cat/cat/tests/main.nf.test.snap | 147 ++++++++++++++ .../cat/tests/nextflow_unzipped_zipped.config | 6 + .../cat/tests/nextflow_zipped_unzipped.config | 8 + modules/nf-core/cat/cat/tests/tags.yml | 2 + modules/nf-core/ltrfinder/environment.yml | 7 + modules/nf-core/ltrfinder/main.nf | 53 +++++ modules/nf-core/ltrfinder/meta.yml | 70 +++++++ modules/nf-core/ltrfinder/tests/main.nf.test | 92 +++++++++ .../nf-core/ltrfinder/tests/main.nf.test.snap | 149 ++++++++++++++ modules/nf-core/ltrharvest/environment.yml | 7 + modules/nf-core/ltrharvest/main.nf | 56 +++++ modules/nf-core/ltrharvest/meta.yml | 68 +++++++ modules/nf-core/ltrharvest/tests/main.nf.test | 89 ++++++++ .../ltrharvest/tests/main.nf.test.snap | 91 +++++++++ .../ltrretriever/ltrretriever/environment.yml | 7 + .../ltrretriever/ltrretriever/meta.yml | 119 +++++++++++ .../ltrretriever/tests/main.nf.test | 186 +++++++++++++++++ .../ltrretriever/tests/nextflow.config | 15 ++ .../builddatabase/environment.yml | 7 + .../repeatmodeler/builddatabase/main.nf | 50 +++++ .../repeatmodeler/builddatabase/meta.yml | 47 +++++ .../builddatabase/tests/main.nf.test | 60 ++++++ .../builddatabase/tests/main.nf.test.snap | 92 +++++++++ .../builddatabase/tests/tags.yml | 2 + .../repeatmodeler/environment.yml | 7 + .../repeatmodeler/repeatmodeler/main.nf | 54 +++++ .../repeatmodeler/repeatmodeler/meta.yml | 68 +++++++ .../repeatmodeler/tests/main.nf.test | 74 +++++++ .../repeatmodeler/tests/main.nf.test.snap | 113 +++++++++++ .../repeatmodeler/tests/tags.yml | 2 + 48 files changed, 2785 insertions(+), 26 deletions(-) create mode 100644 modules/gallvp/annosine/environment.yml create mode 100644 modules/gallvp/annosine/main.nf create mode 100644 modules/gallvp/annosine/meta.yml create mode 100644 modules/gallvp/annosine/tests/main.nf.test create mode 100644 modules/gallvp/annosine/tests/main.nf.test.snap create mode 100644 modules/gallvp/annosine/tests/nextflow.config create mode 100644 modules/gallvp/tirlearner/environment.yml create mode 100644 modules/gallvp/tirlearner/main.nf create mode 100644 modules/gallvp/tirlearner/meta.yml create mode 100644 modules/gallvp/tirlearner/tests/main.nf.test create mode 100644 modules/gallvp/tirlearner/tests/main.nf.test.snap create mode 100644 modules/local/sanitize/main.nf create mode 100644 modules/nf-core/cat/cat/environment.yml create mode 100644 modules/nf-core/cat/cat/main.nf create mode 100644 modules/nf-core/cat/cat/meta.yml create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config create mode 100644 modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config create mode 100644 modules/nf-core/cat/cat/tests/tags.yml create mode 100644 modules/nf-core/ltrfinder/environment.yml create mode 100644 modules/nf-core/ltrfinder/main.nf create mode 100644 modules/nf-core/ltrfinder/meta.yml create mode 100644 modules/nf-core/ltrfinder/tests/main.nf.test create mode 100644 modules/nf-core/ltrfinder/tests/main.nf.test.snap create mode 100644 modules/nf-core/ltrharvest/environment.yml create mode 100644 modules/nf-core/ltrharvest/main.nf create mode 100644 modules/nf-core/ltrharvest/meta.yml create mode 100644 modules/nf-core/ltrharvest/tests/main.nf.test create mode 100644 modules/nf-core/ltrharvest/tests/main.nf.test.snap create mode 100644 modules/nf-core/ltrretriever/ltrretriever/environment.yml create mode 100644 modules/nf-core/ltrretriever/ltrretriever/meta.yml create mode 100644 modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test create mode 100644 modules/nf-core/ltrretriever/ltrretriever/tests/nextflow.config create mode 100644 modules/nf-core/repeatmodeler/builddatabase/environment.yml create mode 100644 modules/nf-core/repeatmodeler/builddatabase/main.nf create mode 100644 modules/nf-core/repeatmodeler/builddatabase/meta.yml create mode 100644 modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test create mode 100644 modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap create mode 100644 modules/nf-core/repeatmodeler/builddatabase/tests/tags.yml create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/environment.yml create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/main.nf create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/meta.yml create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test.snap create mode 100644 modules/nf-core/repeatmodeler/repeatmodeler/tests/tags.yml diff --git a/bin/EDTA_raw.pl b/bin/EDTA_raw.pl index 31c3cf0..c011985 100755 --- a/bin/EDTA_raw.pl +++ b/bin/EDTA_raw.pl @@ -87,16 +87,11 @@ my $trf = ''; #path to trf my $GRF = ''; #path to GRF my $annosine = ""; #path to the AnnoSINE program - -# my $TIR_Learner = "$script_path/bin/TIR-Learner3/"; #tianyulu -# my $LTR_FINDER = "$script_path/bin/LTR_FINDER_parallel/LTR_FINDER_parallel"; #tianyulu -# my $LTR_HARVEST = "$script_path/bin/LTR_HARVEST_parallel/LTR_HARVEST_parallel"; #tianyulu -my $HelitronScanner_Runner = "$script_path/bin/run_helitron_scanner.sh"; - my $TIR_Learner = ""; #path to TIR-Learner3 program #tianyulu my $LTR_FINDER = ""; #path to LTR_FINDER_parallel program #tianyulu my $LTR_HARVEST = ""; #path to LTR_HARVEST_parallel program #tianyulu my $HelitronScanner = ""; #path to HelitronScanner program #tianyulu +my $HelitronScanner_Runner = "$script_path/bin/run_helitron_scanner.sh"; my $help = undef; @@ -160,9 +155,6 @@ print STDERR "$date\tEDTA_raw: Check dependencies, prepare working directories.\n\n"; # check files and dependencies -# die "The LTR_FINDER_parallel is not found in $LTR_FINDER!\n" unless -s $LTR_FINDER; #tianyulu -# die "The LTR_HARVEST_parallel is not found in $LTR_HARVEST!\n" unless -s $LTR_HARVEST; #tianyulu -# die "The TIR_Learner is not found in $TIR_Learner!\n" unless -s "$TIR_Learner/bin/main.py"; #tianyulu die "The script get_range.pl is not found in $get_range!\n" unless -s $get_range; die "The script rename_LTR_skim.pl is not found in $rename_LTR!\n" unless -s $rename_LTR; die "The script filter_gff3.pl is not found in $filter_gff!\n" unless -s $filter_gff; @@ -171,7 +163,6 @@ die "The script rename_tirlearner.pl is not found in $rename_tirlearner!\n" unless -s $rename_tirlearner; die "The script cleanup_tandem.pl is not found in $cleanup_tandem!\n" unless -s $cleanup_tandem; die "The script get_ext_seq.pl is not found in $get_ext_seq!\n" unless -s $get_ext_seq; -# die "The HelitronScanner is not found in $HelitronScanner!\n" unless -s $HelitronScanner; #tianyulu die "The script format_helitronscanner_out.pl is not found in $format_helitronscanner!\n" unless -s $format_helitronscanner; die "The script flanking_filter.pl is not found in $flank_filter!\n" unless -s $flank_filter; die "The script bed2gff.pl is not found in $bed2gff!\n" unless -s $bed2gff; @@ -190,7 +181,6 @@ $repeatmasker = dirname($repeatmasker) unless -d $repeatmasker; $repeatmasker="$repeatmasker/" if $repeatmasker ne '' and $repeatmasker !~ /\/$/; die "Error: RepeatMasker is not found in the RepeatMasker path $repeatmasker!\n" unless -X "${repeatmasker}RepeatMasker"; -# `cp $script_path/database/dummy060817.fa ./dummy060817.fa.$rand`; `cp \"$script_path/database/dummy060817.fa\" ./dummy060817.fa.$rand`; #tianyulu my $RM_test=`${repeatmasker}RepeatMasker -e ncbi -q -pa 1 -no_is -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand 2>/dev/null`; die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/done//gi; @@ -245,14 +235,6 @@ `${grfp}grf-main 2>/dev/null`; die "Error: The Generic Repeat Finder (GRF) is not found in the GRF path: $grfp\n" if $?==32256; -# # TIR-Learner3 -# chomp ($TIR_Learner = `which TIR-Learner 2>/dev/null`) if $TIR_Learner eq ''; -# $TIR_Learner =~ s/\n$//; -# my $tirp= dirname ($TIR_Learner); -# $tirp =~ s/\n$//; -# `${tirp}TIR-Learner 2>/dev/null`; -# die "Error: TIR-Learner3 is not found in the TIR-Learner path: $tirp\n" if $?==32256; - # TIR-Learner #tianyuLu # Remove any trailing whitespace $TIR_Learner =~ s/\s+$//; @@ -260,14 +242,10 @@ # Find TIR-Learner path and remove any trailing newline chomp ($TIR_Learner=`command -v TIR-Learner 2>/dev/null`); die "Error: TIR-Learner not installed!\n" if $TIR_Learner eq ""; - # $TIR_Learner =~ s/\s+$//; } else { # # Extract directory name from path if path is not a directory - # $TIR_Learner = dirname($TIR_Learner) unless -d $TIR_Learner; # If path is directory if (-d $TIR_Learner) { - # # Add trailing slash if path not empty string and not already end with slash - # $TIR_Learner .= "/" if $TIR_Learner ne "" and $TIR_Learner !~ /\/$/; # Add trailing slash if path not already end with slash $TIR_Learner .= "/" if $TIR_Learner !~ /\/$/; $TIR_Learner = "python3 $TIR_Learner/TIR-Learner.py"; @@ -715,7 +693,12 @@ print STDERR "$date\tIdentify Helitron candidates from scratch.\n\n"; # run HelitronScanner -`$HelitronScanner_Runner $genome $threads \"$HelitronScanner\"`; +if ($overwrite eq 0 and (-s "$genome.HelitronScanner.draw.hel.fa" and -s "$genome.HelitronScanner.draw.rc.hel.fa")){ +#cat $genome.HelitronScanner.draw.hel.fa $genome.HelitronScanner.draw.rc.hel.fa + print STDERR "$date\tExisting HelitronScanner result files $genome.HelitronScanner.draw.hel.fa $genome.HelitronScanner.draw.rc.hel.fa found!\n\t\tWill keep these files without rerunning HelitronScanner\n\t\tPlease specify --overwrite 1 if you want to rerun this module.\n\n"; + } else { + `$HelitronScanner_Runner $genome $threads \"$HelitronScanner\"`; + } # filter candidates based on repeatness of flanking regions `perl $format_helitronscanner -genome $genome -sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1`; diff --git a/bin/setup_LTR_retriever_postprocess.sh b/bin/setup_LTR_retriever_postprocess.sh index 140b4b5..66e1cf5 100755 --- a/bin/setup_LTR_retriever_postprocess.sh +++ b/bin/setup_LTR_retriever_postprocess.sh @@ -19,8 +19,8 @@ my \$filter_gff = '$script_path/filter_gff3.pl'; EOF -sed -n 443,462p "$script_path/EDTA_raw.pl" \ +sed -n 421,440p "$script_path/EDTA_raw.pl" \ >> input/LTR_retriever_postprocess.pl -sed -n 466,472p "$script_path/EDTA_raw.pl" \ +sed -n 445,450p "$script_path/EDTA_raw.pl" \ >> input/LTR_retriever_postprocess.pl diff --git a/modules/gallvp/annosine/environment.yml b/modules/gallvp/annosine/environment.yml new file mode 100644 index 0000000..9aef5ec --- /dev/null +++ b/modules/gallvp/annosine/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - "bioconda::annosine2=2.0.7" diff --git a/modules/gallvp/annosine/main.nf b/modules/gallvp/annosine/main.nf new file mode 100644 index 0000000..6408b28 --- /dev/null +++ b/modules/gallvp/annosine/main.nf @@ -0,0 +1,58 @@ +process ANNOSINE { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/annosine2:2.0.7--pyh7cba7a3_0': + 'biocontainers/annosine2:2.0.7--pyh7cba7a3_0' }" + + input: + tuple val(meta), path(fasta) + val mode + + output: + tuple val(meta), path("*.fa") , emit: fa , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.7' // WARN: Manually update when changing Bioconda assets + if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + AnnoSINE_v2 \\ + $args \\ + --threads $task.cpus \\ + $mode \\ + $fasta \\ + $prefix + + mv \\ + $prefix/Seed_SINE.fa \\ + ${prefix}.fa \\ + || echo 'AnnoSINE_v2 did not find SINE sequences. See log for details!' + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + annosine: $VERSION + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.7' // WARN: Manually update when changing Bioconda assets + if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + annosine: $VERSION + END_VERSIONS + """ +} diff --git a/modules/gallvp/annosine/meta.yml b/modules/gallvp/annosine/meta.yml new file mode 100644 index 0000000..ad205b5 --- /dev/null +++ b/modules/gallvp/annosine/meta.yml @@ -0,0 +1,51 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "annosine" +description: Accelerating de novo SINE annotation in plant and animal genomes +keywords: + - genomics + - SINE + - annotation + - plant +tools: + - "annosine": + description: "AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes" + homepage: "https://github.com/liaoherui/AnnoSINE_v2" + documentation: "https://github.com/liaoherui/AnnoSINE_v2" + tool_dev_url: "https://github.com/liaoherui/AnnoSINE_v2" + doi: "10.1101/2024.03.01.582874" + licence: ["MIT"] + identifier: biotools:annosine + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input genome assembly + pattern: "*.{fasta,fa,fsa}" + - - mode: + type: integer + description: Run mode +output: + - fa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.fa": + type: file + description: Non-redundant SINE library with serial number + pattern: "*.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/annosine/tests/main.nf.test b/modules/gallvp/annosine/tests/main.nf.test new file mode 100644 index 0000000..3bafb5d --- /dev/null +++ b/modules/gallvp/annosine/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process ANNOSINE" + script "../main.nf" + process "ANNOSINE" + + tag "modules" + tag "modules_gallvp" + tag "annosine" + + test("actinidia_chinensis - fasta") { + + config './nextflow.config' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + input[1] = 3 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("actinidia_chinensis - fasta - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + input[1] = 3 + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/gallvp/annosine/tests/main.nf.test.snap b/modules/gallvp/annosine/tests/main.nf.test.snap new file mode 100644 index 0000000..4c87403 --- /dev/null +++ b/modules/gallvp/annosine/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "actinidia_chinensis - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,fc3bd39555133a1b50623bccc7d4cf9b" + ] + ], + "1": [ + "versions.yml:md5,e4a37dd3eccd5ff39c2262542db40e98" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,fc3bd39555133a1b50623bccc7d4cf9b" + ] + ], + "versions": [ + "versions.yml:md5,e4a37dd3eccd5ff39c2262542db40e98" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:32:32.714269" + }, + "actinidia_chinensis - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e4a37dd3eccd5ff39c2262542db40e98" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e4a37dd3eccd5ff39c2262542db40e98" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:32:37.586287" + } +} \ No newline at end of file diff --git a/modules/gallvp/annosine/tests/nextflow.config b/modules/gallvp/annosine/tests/nextflow.config new file mode 100644 index 0000000..efdc449 --- /dev/null +++ b/modules/gallvp/annosine/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: ANNOSINE { + ext.args = '-a 2 -rpm 0 --copy_number 1 --shift 200' + } +} diff --git a/modules/gallvp/tirlearner/environment.yml b/modules/gallvp/tirlearner/environment.yml new file mode 100644 index 0000000..d60c615 --- /dev/null +++ b/modules/gallvp/tirlearner/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::tir-learner=3.0.3" diff --git a/modules/gallvp/tirlearner/main.nf b/modules/gallvp/tirlearner/main.nf new file mode 100644 index 0000000..c253245 --- /dev/null +++ b/modules/gallvp/tirlearner/main.nf @@ -0,0 +1,75 @@ +process TIRLEARNER { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/tir-learner:3.0.3--hdfd78af_0': + 'biocontainers/tir-learner:3.0.3--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + val species + + output: + tuple val(meta), path("${prefix}.log") , emit: log + tuple val(meta), path("${prefix}.fa") , emit: fasta , optional: true + tuple val(meta), path("${prefix}.gff3") , emit: gff , optional: true + tuple val(meta), path("${prefix}.filtered.fa") , emit: filtered_fasta , optional: true + tuple val(meta), path("${prefix}.filtered.gff3"), emit: filtered_gff , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def is_zipped = fasta.toString().endsWith('.gz') + def input_name = "$fasta" - ( is_zipped ? '.gz' : '' ) + def unzip_fasta = is_zipped ? "gzip -cdf $fasta > $input_name" : '' + + if ( "$input_name" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + $unzip_fasta + + TIR-Learner \\ + -f $input_name \\ + -s $species \\ + -t $task.cpus \\ + -o $prefix \\ + $args \\ + &> >(tee "${prefix}.log" 2>&1) \\ + || echo "TIR-Learner failed! See ${prefix}.log" + + mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn.fa" "${prefix}.fa" || echo "TIR-Learner failed to find TIRs. See ${prefix}.log" + mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn.gff3" "${prefix}.gff3" || echo "TIR-Learner failed to find TIRs. See ${prefix}.log" + + mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn_filter.fa" "${prefix}.filtered.fa" || echo "TIR-Learner failed to find TIRs. See ${prefix}.log" + mv "${prefix}/TIR-Learner-Result/TIR-Learner_FinalAnn_filter.gff3" "${prefix}.filtered.gff3" || echo "TIR-Learner failed to find TIRs. See ${prefix}.log" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.log + + touch "${prefix}.fa" + touch "${prefix}.gff3" + + touch "${prefix}.filtered.fa" + touch "${prefix}.filtered.gff3" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //') + END_VERSIONS + """ +} diff --git a/modules/gallvp/tirlearner/meta.yml b/modules/gallvp/tirlearner/meta.yml new file mode 100644 index 0000000..ff2c9c2 --- /dev/null +++ b/modules/gallvp/tirlearner/meta.yml @@ -0,0 +1,94 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "tirlearner" +description: | + Ensemble Method for TIR Transposable Element Annotation +keywords: + - genomics + - annotation + - repeat + - transposable +tools: + - "TIR-Learner": + description: TIR-Learner + homepage: "https://github.com/lutianyu2001/TIR-Learner" + documentation: "https://github.com/lutianyu2001/TIR-Learner" + tool_dev_url: "https://github.com/lutianyu2001/TIR-Learner" + doi: "10.1016/j.molp.2019.02.008" + licence: ["GPLv3"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome sequences in fasta format + pattern: "*.{fsa,fa,fasta}" + - - species: + type: string + description: | + "maize", "rice" or "others" +output: + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.log: + type: file + description: Log from TIR-Learner + pattern: "*.log" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.fa: + type: file + description: Putative TIRs in fasta format + pattern: "*.fa" + - gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.gff3: + type: file + description: Putative TIRs in GFF3 format + pattern: "*.gff3" + - filtered_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.filtered.fa: + type: file + description: Filtered TIRs in fasta format + pattern: "*.fa" + - filtered_gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.filtered.gff3: + type: file + description: Filtered TIRs in GFF3 format + pattern: "*.gff3" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jguhlin" + - "@GallVp" +maintainers: + - "@jguhlin" + - "@GallVp" diff --git a/modules/gallvp/tirlearner/tests/main.nf.test b/modules/gallvp/tirlearner/tests/main.nf.test new file mode 100644 index 0000000..034fbac --- /dev/null +++ b/modules/gallvp/tirlearner/tests/main.nf.test @@ -0,0 +1,91 @@ +nextflow_process { + + name "Test Process TIRLEARNER" + script "../main.nf" + process "TIRLEARNER" + + tag "modules" + tag "modules_gallvp" + tag "tirlearner" + + + test("actinidia_chinensis-genome_1_fasta_gz-success") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + input[1] = 'others' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('Module 4 Begin') }, + { assert snapshot( + process.out.fasta, + process.out.gff, + process.out.filtered_fasta, + process.out.filtered_gff, + process.out.versions + ).match() + } + ) + } + + } + + test("sarscov2-genome") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = 'others' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('ValueError: All objects passed were None') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + input[1] = 'others' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/gallvp/tirlearner/tests/main.nf.test.snap b/modules/gallvp/tirlearner/tests/main.nf.test.snap new file mode 100644 index 0000000..dd1a6d0 --- /dev/null +++ b/modules/gallvp/tirlearner/tests/main.nf.test.snap @@ -0,0 +1,155 @@ +{ + "sarscov2-genome": { + "content": [ + [ + "versions.yml:md5,9db74013377c09d8452530315592acdf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T13:03:25.394783" + }, + "actinidia_chinensis-genome_1_fasta_gz-success": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,65987decb67d1e3f95b993f86d14c0d0" + ] + ], + [ + [ + { + "id": "test" + }, + "test.gff3:md5,90bf040e7b29763351237207297dc801" + ] + ], + [ + [ + { + "id": "test" + }, + "test.filtered.fa:md5,65987decb67d1e3f95b993f86d14c0d0" + ] + ], + [ + [ + { + "id": "test" + }, + "test.filtered.gff3:md5,90bf040e7b29763351237207297dc801" + ] + ], + [ + "versions.yml:md5,9db74013377c09d8452530315592acdf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T13:21:08.136874" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.filtered.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.filtered.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,9db74013377c09d8452530315592acdf" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "filtered_fasta": [ + [ + { + "id": "test" + }, + "test.filtered.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "filtered_gff": [ + [ + { + "id": "test" + }, + "test.filtered.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9db74013377c09d8452530315592acdf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T12:56:16.022839" + } +} \ No newline at end of file diff --git a/modules/local/sanitize/main.nf b/modules/local/sanitize/main.nf new file mode 100644 index 0000000..c1519af --- /dev/null +++ b/modules/local/sanitize/main.nf @@ -0,0 +1,38 @@ +// Rename FASTA headers (just makes everything easier later) + +process SANITIZE_HEADERS { + tag "$meta.id" + label 'process_single' + + // Eventually port fffx (pronounced f3x) to bioconda + // conda "${moduleDir}/environment.yml" + // container "docker.io/gallvp/edta-components:v0.1" + + container "${ workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' + ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' + : 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path('*.sanitized.fasta'), emit: fasta + tuple val(meta), path('*.sanitized.translation_table.tsv'), emit: translation_table + eval('fffx --version'), topic: versions + + + when: + task.ext.when == null || task.ext.when + + script: + """ + fffx length-filter ${fasta} filtered.fa 1000 + fffx sanitize filtered.fa ${fasta.baseName}.sanitized + """ + + stub: + """ + touch ${fasta.baseName}.sanitized.fasta + touch ${fasta.baseName}.sanitized.translation_table.tsv + """ +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 0000000..9b01c86 --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf new file mode 100644 index 0000000..2862c64 --- /dev/null +++ b/modules/nf-core/cat/cat/main.nf @@ -0,0 +1,78 @@ +process CAT_CAT { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : + 'biocontainers/pigz:2.3.4' }" + + input: + tuple val(meta), path(files_in) + + output: + tuple val(meta), path("${prefix}"), emit: file_out + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def file_list = files_in.collect { it.toString() } + + // choose appropriate concatenation tool depending on input and output format + + // | input | output | command1 | command2 | + // |-----------|------------|----------|----------| + // | gzipped | gzipped | cat | | + // | ungzipped | ungzipped | cat | | + // | gzipped | ungzipped | zcat | | + // | ungzipped | gzipped | cat | pigz | + + // Use input file ending as default + prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" + out_zip = prefix.endsWith('.gz') + in_zip = file_list[0].endsWith('.gz') + command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' + command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : '' + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + $command1 \\ + $args \\ + ${file_list.join(' ')} \\ + $command2 \\ + > ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + + stub: + def file_list = files_in.collect { it.toString() } + prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + touch $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ +} + +// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz +def getFileSuffix(filename) { + def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ + return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) +} diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml new file mode 100644 index 0000000..81778a0 --- /dev/null +++ b/modules/nf-core/cat/cat/meta.yml @@ -0,0 +1,43 @@ +name: cat_cat +description: A module for concatenation of gzipped or uncompressed files +keywords: + - concatenate + - gzip + - cat +tools: + - cat: + description: Just concatenation + documentation: https://man7.org/linux/man-pages/man1/cat.1.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" +output: + - file_out: + - meta: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - ${prefix}: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@erikrikarddaniel" + - "@FriederikeHanssen" +maintainers: + - "@erikrikarddaniel" + - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test new file mode 100644 index 0000000..9cb1617 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -0,0 +1,191 @@ +nextflow_process { + + name "Test Process CAT_CAT" + script "../main.nf" + process "CAT_CAT" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/cat" + + test("test_cat_name_conflict") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'genome', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("test_cat_unzipped_unzipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap new file mode 100644 index 0000000..b7623ee --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -0,0 +1,147 @@ +{ + "test_cat_unzipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2023-10-16T14:32:18.500464399" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2023-10-16T14:32:49.642741302" + }, + "test_cat_zipped_zipped": { + "content": [ + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ], + 78, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:46.802978" + }, + "test_cat_name_conflict": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:29.45394" + }, + "test_cat_one_file_unzipped_zipped": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ], + 374, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:52:02.774016" + }, + "test_cat_unzipped_zipped": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ], + 375, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:57.581523" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config new file mode 100644 index 0000000..ec26b0f --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config new file mode 100644 index 0000000..fbc7978 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,8 @@ + +process { + + withName: CAT_CAT { + ext.prefix = 'cat.txt' + } + +} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml new file mode 100644 index 0000000..37b578f --- /dev/null +++ b/modules/nf-core/cat/cat/tests/tags.yml @@ -0,0 +1,2 @@ +cat/cat: + - modules/nf-core/cat/cat/** diff --git a/modules/nf-core/ltrfinder/environment.yml b/modules/nf-core/ltrfinder/environment.yml new file mode 100644 index 0000000..2932d5c --- /dev/null +++ b/modules/nf-core/ltrfinder/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::ltr_finder_parallel=1.1" diff --git a/modules/nf-core/ltrfinder/main.nf b/modules/nf-core/ltrfinder/main.nf new file mode 100644 index 0000000..3e59e3c --- /dev/null +++ b/modules/nf-core/ltrfinder/main.nf @@ -0,0 +1,53 @@ +process LTRFINDER { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ltr_finder_parallel:1.1--hdfd78af_0': + 'biocontainers/ltr_finder_parallel:1.1--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.scn") , emit: scn + tuple val(meta), path("*.gff3") , emit: gff + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + LTR_FINDER_parallel \\ + -seq $fasta \\ + -threads $task.cpus \\ + $args + + mv "${fasta}.finder.combine.scn" "${prefix}.scn" + mv "${fasta}.finder.combine.gff3" "${prefix}.gff3" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_FINDER_parallel: \$(LTR_FINDER_parallel -h | grep 'Version:' | sed 's/Version: //') + ltr_finder: \$(ltr_finder -h 2>&1 | grep 'ltr_finder' | sed 's/ltr_finder //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.scn" + touch "${prefix}.gff3" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_FINDER_parallel: \$(LTR_FINDER_parallel -h | grep 'Version:' | sed 's/Version: //') + ltr_finder: \$(ltr_finder -h 2>&1 | grep 'ltr_finder' | sed 's/ltr_finder //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/ltrfinder/meta.yml b/modules/nf-core/ltrfinder/meta.yml new file mode 100644 index 0000000..547fb67 --- /dev/null +++ b/modules/nf-core/ltrfinder/meta.yml @@ -0,0 +1,70 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "ltrfinder" +description: | + Finds full-length LTR retrotranspsons in genome sequences using the + parallel version of LTR_Finder +keywords: + - genomics + - annotation + - parallel + - repeat + - long terminal retrotransposon + - retrotransposon +tools: + - "LTR_FINDER_parallel": + description: A Perl wrapper for LTR_FINDER + homepage: "https://github.com/oushujun/LTR_FINDER_parallel" + documentation: "https://github.com/oushujun/LTR_FINDER_parallel" + tool_dev_url: "https://github.com/oushujun/LTR_FINDER_parallel" + doi: "10.1186/s13100-019-0193-0" + licence: ["MIT"] + identifier: "" + - "LTR_Finder": + description: An efficient program for finding full-length LTR retrotranspsons + in genome sequences + homepage: "https://github.com/xzhub/LTR_Finder" + documentation: "https://github.com/xzhub/LTR_Finder" + tool_dev_url: "https://github.com/xzhub/LTR_Finder" + doi: "10.1093/nar/gkm286" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome sequences in fasta format + pattern: "*.{fsa,fa,fasta}" +output: + - scn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Annotation in LTRharvest or LTR_FINDER format + pattern: "*.scn" + - gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Annotation in gff3 format + pattern: "*.gff3" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test new file mode 100644 index 0000000..dc8c803 --- /dev/null +++ b/modules/nf-core/ltrfinder/tests/main.nf.test @@ -0,0 +1,92 @@ +nextflow_process { + + name "Test Process LTRFINDER" + script "../main.nf" + process "LTRFINDER" + + tag "modules" + tag "modules_nfcore" + tag "ltrfinder" + tag "gunzip" + + test("actinidia_chinensis-genome_21_fasta_gz-success") { + + setup { + run('GUNZIP') { + script "../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2-genome_fasta-no_ltr") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test.snap b/modules/nf-core/ltrfinder/tests/main.nf.test.snap new file mode 100644 index 0000000..0f1790f --- /dev/null +++ b/modules/nf-core/ltrfinder/tests/main.nf.test.snap @@ -0,0 +1,149 @@ +{ + "actinidia_chinensis-genome_21_fasta_gz-success": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.scn:md5,006193c9eaf3f552ccb0369f159e7660" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.gff3:md5,96e5305163939e4381e1b94b660dc0a2" + ] + ], + "2": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ], + "gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,96e5305163939e4381e1b94b660dc0a2" + ] + ], + "scn": [ + [ + { + "id": "test" + }, + "test.scn:md5,006193c9eaf3f552ccb0369f159e7660" + ] + ], + "versions": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:14:38.509965" + }, + "sarscov2-genome_fasta-no_ltr": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.scn:md5,2ce449dff751e59dbc292b6888491954" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.gff3:md5,bddeb04277af08b5850e64708e8af02a" + ] + ], + "2": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ], + "gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,bddeb04277af08b5850e64708e8af02a" + ] + ], + "scn": [ + [ + { + "id": "test" + }, + "test.scn:md5,2ce449dff751e59dbc292b6888491954" + ] + ], + "versions": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-16T13:03:03.505263" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ], + "gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "scn": [ + [ + { + "id": "test" + }, + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7b24225b810fa88cfb2a887de11be333" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T09:14:43.054758" + } +} \ No newline at end of file diff --git a/modules/nf-core/ltrharvest/environment.yml b/modules/nf-core/ltrharvest/environment.yml new file mode 100644 index 0000000..c6cac36 --- /dev/null +++ b/modules/nf-core/ltrharvest/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::ltr_harvest_parallel=1.1" diff --git a/modules/nf-core/ltrharvest/main.nf b/modules/nf-core/ltrharvest/main.nf new file mode 100644 index 0000000..1e5e06d --- /dev/null +++ b/modules/nf-core/ltrharvest/main.nf @@ -0,0 +1,56 @@ +process LTRHARVEST { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ltr_harvest_parallel:1.1--hdfd78af_0': + 'biocontainers/ltr_harvest_parallel:1.1--hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.gff3") , emit: gff3 + tuple val(meta), path("*.scn") , emit: scn + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + LTR_HARVEST_parallel \\ + -seq $fasta \\ + $args \\ + -threads $task.cpus + + mv "${fasta}.harvest.combine.gff3" \\ + "${prefix}.gff3" + + mv "${fasta}.harvest.combine.scn" \\ + "${prefix}.scn" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_HARVEST_parallel: \$(LTR_HARVEST_parallel -h | sed -n '/Version/s/Version: //p') + genometools: \$(gt --version | sed '1!d ; s/gt (GenomeTools) //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.gff3" + touch "${prefix}.scn" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + LTR_HARVEST_parallel: \$(LTR_HARVEST_parallel -h | sed -n '/Version/s/Version: //p') + genometools: \$(gt --version | sed '1!d ; s/gt (GenomeTools) //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/ltrharvest/meta.yml b/modules/nf-core/ltrharvest/meta.yml new file mode 100644 index 0000000..1806418 --- /dev/null +++ b/modules/nf-core/ltrharvest/meta.yml @@ -0,0 +1,68 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "ltrharvest" +description: | + Predicts LTR retrotransposons using the parallel version of GenomeTools gt-ltrharvest + utility included in the EDTA toolchain +keywords: + - genomics + - genome + - annotation + - repeat + - transposons + - retrotransposons +tools: + - "LTR_HARVEST_parallel": + description: A Perl wrapper for LTR_harvest + homepage: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" + documentation: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" + tool_dev_url: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" + licence: ["MIT"] + identifier: "" + - "gt": + description: "The GenomeTools genome analysis system" + homepage: "https://genometools.org/index.html" + documentation: "https://genometools.org/documentation.html" + tool_dev_url: "https://github.com/genometools/genometools" + doi: "10.1109/TCBB.2013.68" + licence: ["ISC"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input genome fasta + pattern: "*.{fsa,fa,fasta}" +output: + - gff3: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Predicted LTR candidates in gff3 format + pattern: "*.gff3" + - scn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Predicted LTR candidates in scn format + pattern: "*.scn" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/nf-core/ltrharvest/tests/main.nf.test b/modules/nf-core/ltrharvest/tests/main.nf.test new file mode 100644 index 0000000..e200fde --- /dev/null +++ b/modules/nf-core/ltrharvest/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + + name "Test Process LTRHARVEST" + script "../main.nf" + process "LTRHARVEST" + + tag "modules" + tag "modules_nfcore" + tag "ltrharvest" + + test("homo_sapiens - genome_21_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gff3, + process.out.versions + ).match() + }, + { assert path(process.out.scn[0][1]).text.contains("46510803 46520182 9380 46510803 46510940 138 46520042 46520182 141 86.52 0 chr21") }, + ) + } + + } + + test("sarscov2 - genome_fasta - no_ltr") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gff3, + process.out.versions + ).match() + }, + { assert path(process.out.scn[0][1]).text.contains("predictions are reported in the following way") }, + ) + } + + } + + test("homo_sapiens - genome_fasta - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/ltrharvest/tests/main.nf.test.snap b/modules/nf-core/ltrharvest/tests/main.nf.test.snap new file mode 100644 index 0000000..f3a8da8 --- /dev/null +++ b/modules/nf-core/ltrharvest/tests/main.nf.test.snap @@ -0,0 +1,91 @@ +{ + "sarscov2 - genome_fasta - no_ltr": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gff3:md5,bddeb04277af08b5850e64708e8af02a" + ] + ], + [ + "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-17T10:40:36.380052" + }, + "homo_sapiens - genome_fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc" + ], + "gff3": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "scn": [ + [ + { + "id": "test" + }, + "test.scn:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-17T10:40:40.967557" + }, + "homo_sapiens - genome_21_fasta": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gff3:md5,da13c4ba22e44ef944ddec38aa72c468" + ] + ], + [ + "versions.yml:md5,51e82185b713482d1d48b6f15abe7fcc" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-17T10:40:30.946" + } +} \ No newline at end of file diff --git a/modules/nf-core/ltrretriever/ltrretriever/environment.yml b/modules/nf-core/ltrretriever/ltrretriever/environment.yml new file mode 100644 index 0000000..f1c392a --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::LTR_retriever=2.9.9" diff --git a/modules/nf-core/ltrretriever/ltrretriever/meta.yml b/modules/nf-core/ltrretriever/ltrretriever/meta.yml new file mode 100644 index 0000000..9645de2 --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/meta.yml @@ -0,0 +1,119 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "ltrretriever_ltrretriever" +description: Identifies LTR retrotransposons using LTR_retriever +keywords: + - genomics + - annotation + - repeat + - long terminal repeat + - retrotransposon +tools: + - "LTR_retriever": + description: Sensitive and accurate identification of LTR retrotransposons + homepage: "https://github.com/oushujun/LTR_retriever" + documentation: "https://github.com/oushujun/LTR_retriever" + tool_dev_url: "https://github.com/oushujun/LTR_retriever" + doi: "10.1104/pp.17.01310" + licence: ["GPL v3"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - genome: + type: file + description: Genomic sequences in fasta format + pattern: "*.{fsa,fa,fasta}" + - - harvest: + type: file + description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular + format + pattern: "*.tabout" + - - finder: + type: file + description: LTR-RT candidates from LTR_FINDER + pattern: "*.scn" + - - mgescan: + type: file + description: LTR-RT candidates from MGEScan_LTR + pattern: "*.out" + - - non_tgca: + type: file + description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in + the old tabular format + pattern: "*.tabout" +output: + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Output log from LTR_retriever + pattern: "*.log" + - pass_list: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.pass.list: + type: file + description: Intact LTR-RTs with coordinate and structural information in summary + table format + pattern: "*.pass.list" + - pass_list_gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.pass.list.gff3": + type: file + description: Intact LTR-RTs with coordinate and structural information in gff3 + format + pattern: "*.pass.list.gff3" + - ltrlib: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.LTRlib.fa": + type: file + description: All non-redundant LTR-RTs + pattern: "*.LTRlib.fa" + - annotation_out: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.out: + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library + pattern: "*.out" + - annotation_gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.out.gff3": + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library in + gff3 format + pattern: "*.out.gff3" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test new file mode 100644 index 0000000..4d512f3 --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test @@ -0,0 +1,186 @@ +nextflow_process { + + name "Test Process LTRRETRIEVER_LTRRETRIEVER" + script "../main.nf" + process "LTRRETRIEVER_LTRRETRIEVER" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ltrretriever" + tag "ltrretriever/ltrretriever" + tag "gunzip" + tag "ltrharvest" + tag "ltrfinder" + tag "cat/cat" + + test("sarscov2-genome-no_ltr") { + + setup { + + run("LTRHARVEST") { + script "../../../ltrharvest/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + run("LTRFINDER") { + script "../../../ltrfinder/main.nf" + + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + run("CAT_CAT") { + script "../../../cat/cat/main.nf" + + process { + """ + input[0] = LTRHARVEST.out.scn.mix(LTRFINDER.out.scn).groupTuple() + """ + } + } + } + + when { + process { + """ + input[0] = input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = CAT_CAT.out.file_out.map { meta, tabout -> tabout } + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("ERROR: No candidate is found in the file(s) you specified.") }, + { assert snapshot(process.out.versions).match("versions_no_ltr") } + ) + } + + } + + test("actinidia_chinensis-genome_21_fasta_gz-success") { + + setup { + + run('GUNZIP') { + script "../../../gunzip/main.nf" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + run("LTRHARVEST") { + script "../../../ltrharvest/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + run("LTRFINDER") { + script "../../../ltrfinder/main.nf" + + process { + """ + input[0] = GUNZIP.out.gunzip + """ + } + } + + run("CAT_CAT") { + script "../../../cat/cat/main.nf" + + process { + """ + input[0] = LTRHARVEST.out.scn.mix(LTRFINDER.out.scn).groupTuple() + """ + } + } + } + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + input[1] = CAT_CAT.out.file_out.map { meta, tabout -> tabout } + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.log[0][1]).text.contains("####### Result files #########") }, + { assert path(process.out.pass_list[0][1]).text.contains("Copia\tLTR") }, + { assert path(process.out.pass_list_gff[0][1]).text.contains("chr1\tLTR_retriever\ttarget_site_duplication") }, + { assert path(process.out.ltrlib[0][1]).text.contains("LTR#LTR/Copia") }, + { assert snapshot(process.out.annotation_out).match("annotation_out") }, + { assert path(process.out.annotation_gff[0][1]).text.contains("Classification=LTR/Copia") }, + { assert snapshot(path(process.out.versions[0]).text).match("versions") } + ) + } + + } + + test("stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/nextflow.config b/modules/nf-core/ltrretriever/ltrretriever/tests/nextflow.config new file mode 100644 index 0000000..7f67556 --- /dev/null +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/nextflow.config @@ -0,0 +1,15 @@ +process { + + withName: LTRFINDER { + ext.args = '-harvest_out' + // LTRRETRIEVER_LTRRETRIEVER requires -harvest_out + } + + withName: LTRHARVEST { + ext.prefix = { "${meta.id}_ltrharvest" } + } + + withName: CAT_CAT { + ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } + } +} diff --git a/modules/nf-core/repeatmodeler/builddatabase/environment.yml b/modules/nf-core/repeatmodeler/builddatabase/environment.yml new file mode 100644 index 0000000..5314307 --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::repeatmodeler=2.0.5" diff --git a/modules/nf-core/repeatmodeler/builddatabase/main.nf b/modules/nf-core/repeatmodeler/builddatabase/main.nf new file mode 100644 index 0000000..6fe244b --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/main.nf @@ -0,0 +1,50 @@ +process REPEATMODELER_BUILDDATABASE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/repeatmodeler:2.0.5--pl5321hdfd78af_0': + 'biocontainers/repeatmodeler:2.0.5--pl5321hdfd78af_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("${prefix}.*") , emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + """ + BuildDatabase \\ + -name $prefix \\ + $fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.nhr + touch ${prefix}.nin + touch ${prefix}.njs + touch ${prefix}.nnd + touch ${prefix}.nni + touch ${prefix}.nog + touch ${prefix}.nsq + touch ${prefix}.translation + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/repeatmodeler/builddatabase/meta.yml b/modules/nf-core/repeatmodeler/builddatabase/meta.yml new file mode 100644 index 0000000..cc78cf0 --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/meta.yml @@ -0,0 +1,47 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "repeatmodeler_builddatabase" +description: Create a database for RepeatModeler +keywords: + - genomics + - fasta + - repeat +tools: + - "repeatmodeler": + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." + homepage: "https://github.com/Dfam-consortium/RepeatModeler" + documentation: "https://github.com/Dfam-consortium/RepeatModeler" + tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" + licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta,fsa,fa}" +output: + - db: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Database files for repeatmodeler + pattern: "`${prefix}.*`" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test new file mode 100644 index 0000000..78b78a6 --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process REPEATMODELER_BUILDDATABASE" + script "../main.nf" + process "REPEATMODELER_BUILDDATABASE" + + tag "modules" + tag "modules_nfcore" + tag "repeatmodeler" + tag "repeatmodeler/builddatabase" + + test("sarscov2-genome_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(process.out.db[0][1].collect { file(it).name }.sort().toString()).match("db") }, + { assert snapshot(process.out.db[0][1].findAll { ! ( "$it"[-3..-1] in [ 'nin', 'njs' ] ) } ).match("stable_md5") } + ) + } + + } + + test("sarscov2-genome_fasta-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap new file mode 100644 index 0000000..1f1a551 --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/tests/main.nf.test.snap @@ -0,0 +1,92 @@ +{ + "sarscov2-genome_fasta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.nhr:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nin:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.njs:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nnd:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nni:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nog:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nsq:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.translation:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,7944637266bc3e2726899eaad5e46c87" + ], + "db": [ + [ + { + "id": "test" + }, + [ + "test.nhr:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nin:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.njs:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nnd:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nni:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nog:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.nsq:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.translation:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,7944637266bc3e2726899eaad5e46c87" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-02T12:06:44.261566" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,7944637266bc3e2726899eaad5e46c87" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-09T15:14:48.807063" + }, + "stable_md5": { + "content": [ + [ + "test.nhr:md5,1a41cb6d0b00c28f62ad60e75ae2f6fc", + "test.nnd:md5,2002e13acf59079a1a5782c918894579", + "test.nni:md5,26a954ba0fd80983b550d8f6b8b35ff8", + "test.nog:md5,30896f123998e926ea2237b89091e7fe", + "test.nsq:md5,982cbc7d9e38743b9b1037588862b9da", + "test.translation:md5,ccbb119522c09daa976a9015ba999329" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-23T10:03:41.669433" + }, + "db": { + "content": [ + "[test.nhr, test.nin, test.njs, test.nnd, test.nni, test.nog, test.nsq, test.translation]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-02T12:08:36.94713" + } +} \ No newline at end of file diff --git a/modules/nf-core/repeatmodeler/builddatabase/tests/tags.yml b/modules/nf-core/repeatmodeler/builddatabase/tests/tags.yml new file mode 100644 index 0000000..c524294 --- /dev/null +++ b/modules/nf-core/repeatmodeler/builddatabase/tests/tags.yml @@ -0,0 +1,2 @@ +repeatmodeler/builddatabase: + - "modules/nf-core/repeatmodeler/builddatabase/**" diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml new file mode 100644 index 0000000..5314307 --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::repeatmodeler=2.0.5" diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/main.nf b/modules/nf-core/repeatmodeler/repeatmodeler/main.nf new file mode 100644 index 0000000..9d0449f --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/main.nf @@ -0,0 +1,54 @@ +process REPEATMODELER_REPEATMODELER { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/repeatmodeler:2.0.5--pl5321hdfd78af_0': + 'biocontainers/repeatmodeler:2.0.5--pl5321hdfd78af_0' }" + + input: + tuple val(meta), path(db) + + output: + tuple val(meta), path("*.fa") , emit: fasta + tuple val(meta), path("*.stk"), emit: stk + tuple val(meta), path("*.log"), emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def db_name = file(db[0]).getBaseName() + """ + RepeatModeler \\ + -database $db_name \\ + $args \\ + -threads $task.cpus + + mv ${db_name}-families.fa ${prefix}.fa + mv ${db_name}-families.stk ${prefix}.stk + mv ${db_name}-rmod.log ${prefix}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.fa + touch ${prefix}.stk + touch ${prefix}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + repeatmodeler: \$(RepeatModeler --version | sed 's/RepeatModeler version //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml new file mode 100644 index 0000000..6693ae9 --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml @@ -0,0 +1,68 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "repeatmodeler_repeatmodeler" +description: Performs de novo transposable element (TE) family identification with + RepeatModeler +keywords: + - genomics + - fasta + - repeat + - transposable element +tools: + - "repeatmodeler": + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." + homepage: "https://github.com/Dfam-consortium/RepeatModeler" + documentation: "https://github.com/Dfam-consortium/RepeatModeler" + tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" + licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - db: + type: file + description: RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE + pattern: "*" +output: + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.fa": + type: file + description: Consensus repeat sequences + pattern: "*.fa" + - stk: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stk": + type: file + description: Seed alignments + pattern: "*.stk" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: A summarized log of the run + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test new file mode 100644 index 0000000..829e222 --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test @@ -0,0 +1,74 @@ +nextflow_process { + + name "Test Process REPEATMODELER_REPEATMODELER" + script "../main.nf" + process "REPEATMODELER_REPEATMODELER" + + tag "modules" + tag "modules_nfcore" + tag "repeatmodeler" + tag "repeatmodeler/repeatmodeler" + tag "repeatmodeler/builddatabase" + + test("homo_sapiens-genome_fasta") { + + setup { + run("REPEATMODELER_BUILDDATABASE") { + script "../../../../nf-core/repeatmodeler/builddatabase" + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = REPEATMODELER_BUILDDATABASE.out.db + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.fasta).match("fasta") }, + { assert snapshot(process.out.stk).match("stk") }, + { assert file(process.out.log[0][1]).text.contains('1 families discovered.') }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-genome_fasta-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test.snap b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test.snap new file mode 100644 index 0000000..e923952 --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,1bb6846ecf1304c262eaef4d3de60cf9" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-09T15:06:55.753492" + }, + "homo_sapiens-genome_fasta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.stk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,1bb6846ecf1304c262eaef4d3de60cf9" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test" + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stk": [ + [ + { + "id": "test" + }, + "test.stk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1bb6846ecf1304c262eaef4d3de60cf9" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:16:41.45166" + }, + "stk": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.stk:md5,acd01ad35763c11315e2297a4f051d57" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-09T15:06:55.740963" + }, + "fasta": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,e25326771341204e1f8054d9529411e5" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-09T15:06:55.737658" + } +} \ No newline at end of file diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/tests/tags.yml b/modules/nf-core/repeatmodeler/repeatmodeler/tests/tags.yml new file mode 100644 index 0000000..df65110 --- /dev/null +++ b/modules/nf-core/repeatmodeler/repeatmodeler/tests/tags.yml @@ -0,0 +1,2 @@ +repeatmodeler/repeatmodeler: + - "modules/nf-core/repeatmodeler/repeatmodeler/**" From aa5abbb31f52bfd99841cd1a303bf7b900b05c2d Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 12 Dec 2024 13:35:00 +1300 Subject: [PATCH 34/49] Added TIR_LEARNER_POSTPROCESS --- bin/setup_TIR-Learner_postprocess.sh | 28 +++++++ conf/modules.config | 10 +++ .../local/ltr_retriever_postprocess/main.nf | 4 + .../tir_learner_postprocess/environment.yml | 10 +++ modules/local/tir_learner_postprocess/main.nf | 76 +++++++++++++++++++ tests/nf-test/small/main.nf.test | 2 + tests/nf-test/small/main.nf.test.snap | 21 +++-- workflows/edta.nf | 32 ++++++-- 8 files changed, 171 insertions(+), 12 deletions(-) create mode 100755 bin/setup_TIR-Learner_postprocess.sh create mode 100644 modules/local/tir_learner_postprocess/environment.yml create mode 100644 modules/local/tir_learner_postprocess/main.nf diff --git a/bin/setup_TIR-Learner_postprocess.sh b/bin/setup_TIR-Learner_postprocess.sh new file mode 100755 index 0000000..777059f --- /dev/null +++ b/bin/setup_TIR-Learner_postprocess.sh @@ -0,0 +1,28 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/TIR-Learner_postprocess.pl << EOF +my \$genome = 'genome'; +my \$threads = $1; + +my \$rename_tirlearner = "$script_path/rename_tirlearner.pl"; +my \$get_ext_seq = "$script_path/get_ext_seq.pl"; +my \$flank_filter = "$script_path/flanking_filter.pl"; +my \$output_by_list = '$script_path/output_by_list.pl'; +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; +my \$cleanup_misclas = '$script_path/cleanup_misclas.pl'; +my \$bed2gff = "$script_path/bed2gff.pl"; + +my \$blastplus = ''; # Assumed on PATH +my \$mdust = ''; # Assumed on PATH +my \$trf = '$(which trf)'; +my \$TEsorter = ''; # Assumed on PATH + +EOF + +sed -n 632,653p "$script_path/EDTA_raw.pl" \ + >> input/TIR-Learner_postprocess.pl + +sed -n 657,660p "$script_path/EDTA_raw.pl" \ + >> input/TIR-Learner_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index c521005..a854d4e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -52,5 +52,15 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/tir" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf index e679be6..e950b59 100644 --- a/modules/local/ltr_retriever_postprocess/main.nf +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -68,6 +68,10 @@ process LTR_RETRIEVER_POSTPROCESS { def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ + touch ${prefix}.LTR.raw.fa + touch ${prefix}.genome.LTR.intact.raw.fa + touch ${prefix}.LTR.intact.raw.gff3 + touch ${prefix}.LTR.intact.raw.fa.anno.list cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/tir_learner_postprocess/environment.yml b/modules/local/tir_learner_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/tir_learner_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/tir_learner_postprocess/main.nf b/modules/local/tir_learner_postprocess/main.nf new file mode 100644 index 0000000..275fc5a --- /dev/null +++ b/modules/local/tir_learner_postprocess/main.nf @@ -0,0 +1,76 @@ +process TIR_LEARNER_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/TIR-Learner-Result/TIR-Learner_FinalAnn.fa" + path "input/TIR-Learner-Result/TIR-Learner_FinalAnn.gff3" + + output: + tuple val(meta), path('*.TIR.intact.raw.fa') , emit: intact_raw_fa + tuple val(meta), path('*.TIR.intact.raw.gff3') , emit: intact_raw_gff3 + tuple val(meta), path('*.TIR.intact.raw.bed') , emit: intact_raw_bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_TIR-Learner_postprocess.sh \\ + $task.cpus + + cd input + + perl TIR-Learner_postprocess.pl + + cd - + + mv \\ + genome.TIR.intact.raw.fa \\ + ${prefix}.TIR.intact.raw.fa + + mv \\ + genome.TIR.intact.raw.gff3 \\ + ${prefix}.TIR.intact.raw.gff3 + + mv \\ + genome.TIR.intact.raw.bed \\ + ${prefix}.TIR.intact.raw.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.TIR.intact.raw.fa + touch ${prefix}.TIR.intact.raw.gff3 + touch ${prefix}.TIR.intact.raw.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index ce37a4f..d53e28f 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -21,6 +21,8 @@ nextflow_pipeline { 'pipeline_info/*.{html,json,txt,yml}', 'ltr/*.pp.LTR.intact.raw.gff3', 'ltr/*.pp.LTR.raw.fa', + 'tir/*.pp.TIR.intact.raw.fa', + 'tir/*.pp.TIR.intact.raw.gff3', ], null, ['**'] diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index a943b0a..1469232 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 17, + "successful tasks": 18, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -57,13 +57,20 @@ "TIRLEARNER": { "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" }, + "TIR_LEARNER_POSTPROCESS": { + "perl": "v5.32.1", + "trf": 4.09, + "TEsorter": "1.4.7", + "mdust": "2006.10.17" + }, "Workflow": { "jguhlin/EDTA": "v0.1.0dev" } }, "stable paths": [ "genome.pp.LTR.intact.raw.fa.anno.list:md5,51261f020350b448acdf89d8fb625448", - "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25" + "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25", + "genome.pp.TIR.intact.raw.bed:md5,12406184046b11edc2ddadbc82765966" ], "stable names": [ "ltr", @@ -71,14 +78,18 @@ "ltr/genome.pp.LTR.intact.raw.gff3", "ltr/genome.pp.LTR.raw.fa", "ltr/genome.pp.genome.LTR.intact.raw.fa", - "pipeline_info" + "pipeline_info", + "tir", + "tir/genome.pp.TIR.intact.raw.bed", + "tir/genome.pp.TIR.intact.raw.fa", + "tir/genome.pp.TIR.intact.raw.gff3" ] } ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-05T12:10:52.622584" + "timestamp": "2024-12-12T13:06:43.800123" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index a4799cf..58f96d2 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -10,6 +10,7 @@ include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmod include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' +include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' @@ -83,7 +84,8 @@ workflow EDTA { params.species ) - ch_tirlearner_filtered_gff = TIRLEARNER.out.filtered_gff + ch_tirlearner_fasta = TIRLEARNER.out.fasta + ch_tirlearner_gff = TIRLEARNER.out.gff ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) // These can also run in parallel @@ -153,7 +155,7 @@ workflow EDTA { ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) // MODULE: LTR_RETRIEVER_POSTPROCESS - ltr_retriever_postprocess_inputs = ch_sanitized_fasta + ch_ltr_retriever_postprocess_inputs = ch_sanitized_fasta | join(ch_pass_list) | join(ch_pass_list_gff) | join(ch_annotation_gff) @@ -169,15 +171,31 @@ workflow EDTA { } LTR_RETRIEVER_POSTPROCESS ( - ltr_retriever_postprocess_inputs.genome, - ltr_retriever_postprocess_inputs.pass, - ltr_retriever_postprocess_inputs.p_gff, - ltr_retriever_postprocess_inputs.defalse, - ltr_retriever_postprocess_inputs.ltr, + ch_ltr_retriever_postprocess_inputs.genome, + ch_ltr_retriever_postprocess_inputs.pass, + ch_ltr_retriever_postprocess_inputs.p_gff, + ch_ltr_retriever_postprocess_inputs.defalse, + ch_ltr_retriever_postprocess_inputs.ltr, ) ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) + // MODULE: TIR_LEARNER_POSTPROCESS + ch_tir_learner_postprocess_inputs = ch_sanitized_fasta + | join(ch_tirlearner_fasta) + | join(ch_tirlearner_gff) + | multiMap { meta, fasta, tir_fa, tir_gff -> + genome : [ meta, fasta ] + tir_fa : tir_fa + tir_gff : tir_gff + } + TIR_LEARNER_POSTPROCESS ( + ch_tir_learner_postprocess_inputs.genome, + ch_tir_learner_postprocess_inputs.tir_fa, + ch_tir_learner_postprocess_inputs.tir_gff + ) + + ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) // Function: Save versions ch_versions = ch_versions From 295db65bf3630b3a3096096f0f8c079d58271097 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 12 Dec 2024 17:33:00 +1300 Subject: [PATCH 35/49] Added REPEATMODELER_POSTPROCESS --- bin/setup_RepeatModeler_postprocess.sh | 22 ++++++ conf/modules.config | 10 +++ conf/test.config | 2 +- main.nf | 16 +---- .../repeatmodeler_postprocess/environment.yml | 10 +++ .../local/repeatmodeler_postprocess/main.nf | 69 +++++++++++++++++++ tests/nf-test/small/main.nf.test | 2 +- tests/nf-test/tiny/main.nf.test | 2 +- workflows/edta.nf | 17 ++++- 9 files changed, 131 insertions(+), 19 deletions(-) create mode 100755 bin/setup_RepeatModeler_postprocess.sh create mode 100644 modules/local/repeatmodeler_postprocess/environment.yml create mode 100644 modules/local/repeatmodeler_postprocess/main.nf diff --git a/bin/setup_RepeatModeler_postprocess.sh b/bin/setup_RepeatModeler_postprocess.sh new file mode 100755 index 0000000..a601979 --- /dev/null +++ b/bin/setup_RepeatModeler_postprocess.sh @@ -0,0 +1,22 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/RepeatModeler_postprocess.pl << EOF +my \$genome = 'genome'; +my \$threads = $1; + +my \$cleanup_misclas = '$script_path/cleanup_misclas.pl'; +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; +my \$output_by_list = '$script_path/output_by_list.pl'; + +my \$TEsorter = ''; # Assumed on PATH +my \$trf = '$(which trf)'; + +EOF + +sed -n 567,579p "$script_path/EDTA_raw.pl" \ + >> input/RepeatModeler_postprocess.pl + +sed -n 585,586p "$script_path/EDTA_raw.pl" \ + >> input/RepeatModeler_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index a854d4e..6ff3d77 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -62,5 +62,15 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: 'EDTA:REPEATMODELER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/rm2" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/conf/test.config b/conf/test.config index e0a2931..73fe0a6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -7,5 +7,5 @@ process { } params { - genomes = 'https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa' + genome = 'https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa' } \ No newline at end of file diff --git a/main.nf b/main.nf index fa74a8b..6607f9e 100755 --- a/main.nf +++ b/main.nf @@ -2,26 +2,12 @@ nextflow.enable.dsl = 2 -params.genomes = 'genomes/*' +params.genome = 'genomes/*' params.species = 'others' -params.cds = '' -params.curatedlib = '' -params.rmlib = '' -params.sensitive = false -params.anno = false -params.rmout = '' -params.maxdiv = 40 -params.evaluate = true -params.exclude = '' -params.maxint = 5000 params.outdir = 'results' include { EDTA } from './workflows/edta.nf' -// Test run: -// ./main.nf -profile docker,test -// ./main.nf -profile conda,test - workflow { EDTA() } diff --git a/modules/local/repeatmodeler_postprocess/environment.yml b/modules/local/repeatmodeler_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/repeatmodeler_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/repeatmodeler_postprocess/main.nf b/modules/local/repeatmodeler_postprocess/main.nf new file mode 100644 index 0000000..f538422 --- /dev/null +++ b/modules/local/repeatmodeler_postprocess/main.nf @@ -0,0 +1,69 @@ +process REPEATMODELER_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/genome-families.fa" + + output: + tuple val(meta), path('*.RM2.fa') , emit: rm2_fa + tuple val(meta), path('*.LINE.raw.fa') , emit: line_raw + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_RepeatModeler_postprocess.sh \\ + $task.cpus + + cd input + + perl RepeatModeler_postprocess.pl + + cd - + + mv \\ + genome.RM2.fa \\ + ${prefix}.RM2.fa + + mv \\ + genome.LINE.raw.fa \\ + ${prefix}.LINE.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.RM2.fa + touch ${prefix}.LINE.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index d53e28f..01353a0 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { when { params { - genomes = "https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa" + genome = "https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa" outdir = "$outputDir" } } diff --git a/tests/nf-test/tiny/main.nf.test b/tests/nf-test/tiny/main.nf.test index 5022c49..0a92bd5 100644 --- a/tests/nf-test/tiny/main.nf.test +++ b/tests/nf-test/tiny/main.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { when { params { - genomes = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" + genome = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" outdir = "$outputDir" } } diff --git a/workflows/edta.nf b/workflows/edta.nf index 58f96d2..ea91e2e 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -11,6 +11,7 @@ include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main.nf' +include { REPEATMODELER_POSTPROCESS } from '../modules/local/repeatmodeler_postprocess/main.nf' include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' @@ -22,7 +23,7 @@ workflow EDTA { ch_versions = Channel.empty() - ch_genome = Channel.fromPath(params.genomes) + ch_genome = Channel.fromPath(params.genome) // Create a meta object for each genome ch_meta_genome = ch_genome.map { genome -> @@ -197,6 +198,20 @@ workflow EDTA { ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) + // MODULE: REPEATMODELER_POSTPROCESS + ch_repeatmodeler_postprocess_inputs = ch_sanitized_fasta + | join(ch_repeatmodeler_fasta) + | multiMap { meta, fasta, rm_fa -> + genome : [ meta, fasta ] + rm_fa : rm_fa + } + REPEATMODELER_POSTPROCESS ( + ch_repeatmodeler_postprocess_inputs.genome, + ch_repeatmodeler_postprocess_inputs.rm_fa, + ) + + ch_versions = ch_versions.mix(REPEATMODELER_POSTPROCESS.out.versions.first()) + // Function: Save versions ch_versions = ch_versions | unique From d36deb0c4f04da612747d91b1440f53919a87e73 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 12 Dec 2024 18:20:16 +1300 Subject: [PATCH 36/49] Updated snapshots --- tests/nf-test/small/main.nf.test | 2 ++ tests/nf-test/small/main.nf.test.snap | 13 +++++++++++-- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index 01353a0..5e111fb 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -23,6 +23,8 @@ nextflow_pipeline { 'ltr/*.pp.LTR.raw.fa', 'tir/*.pp.TIR.intact.raw.fa', 'tir/*.pp.TIR.intact.raw.gff3', + 'rm2/*.pp.LINE.raw.fa', + 'rm2/*.pp.RM2.fa', ], null, ['**'] diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index 1469232..636069c 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 18, + "successful tasks": 19, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -51,6 +51,12 @@ "REPEATMODELER_BUILDDATABASE": { "repeatmodeler": "2.0.5" }, + "REPEATMODELER_POSTPROCESS": { + "perl": "v5.32.1", + "trf": 4.09, + "TEsorter": "1.4.7", + "mdust": "2006.10.17" + }, "REPEATMODELER_REPEATMODELER": { "repeatmodeler": "2.0.5" }, @@ -79,6 +85,9 @@ "ltr/genome.pp.LTR.raw.fa", "ltr/genome.pp.genome.LTR.intact.raw.fa", "pipeline_info", + "rm2", + "rm2/genome.pp.LINE.raw.fa", + "rm2/genome.pp.RM2.fa", "tir", "tir/genome.pp.TIR.intact.raw.bed", "tir/genome.pp.TIR.intact.raw.fa", @@ -90,6 +99,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-12T13:06:43.800123" + "timestamp": "2024-12-12T18:08:43.061775" } } \ No newline at end of file From f30f663ccd46bb233ed0d6e46d45cc7a1877b328 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 13 Dec 2024 11:13:34 +1300 Subject: [PATCH 37/49] Added HELITRONSCANNER_POSTPROCESS --- bin/setup_HelitronScanner_postprocess.sh | 27 ++ conf/modules.config | 56 +-- conf/test.config | 6 +- .../environment.yml | 10 + .../local/helitronscanner_postprocess/main.nf | 82 +++++ modules/local/utils/main.nf | 23 +- nextflow.config | 8 +- tests/nf-test/small/main.nf.test | 15 +- tests/nf-test/small/main.nf.test.snap | 46 ++- tests/nf-test/tiny/main.nf.test.snap | 11 +- workflows/edta.nf | 324 ++++++++++-------- 11 files changed, 405 insertions(+), 203 deletions(-) create mode 100755 bin/setup_HelitronScanner_postprocess.sh create mode 100644 modules/local/helitronscanner_postprocess/environment.yml create mode 100644 modules/local/helitronscanner_postprocess/main.nf diff --git a/bin/setup_HelitronScanner_postprocess.sh b/bin/setup_HelitronScanner_postprocess.sh new file mode 100755 index 0000000..59df997 --- /dev/null +++ b/bin/setup_HelitronScanner_postprocess.sh @@ -0,0 +1,27 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/HelitronScanner_postprocess.pl << EOF +my \$genome = 'genome'; +my \$threads = $1; + +my \$flank_filter = "$script_path/flanking_filter.pl"; +my \$output_by_list = '$script_path/output_by_list.pl'; +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; +my \$cleanup_misclas = '$script_path/cleanup_misclas.pl'; +my \$make_bed = "$script_path/make_bed_with_intact.pl"; +my \$bed2gff = "$script_path/bed2gff.pl"; + +my \$blastplus = ''; # Assumed on PATH +my \$mdust = ''; # Assumed on PATH +my \$trf = '$(which trf)'; +my \$TEsorter = ''; # Assumed on PATH + +EOF + +sed -n 705,722p "$script_path/EDTA_raw.pl" \ + >> input/HelitronScanner_postprocess.pl + +sed -n 726,729p "$script_path/EDTA_raw.pl" \ + >> input/HelitronScanner_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index 6ff3d77..ff251a2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -11,6 +11,26 @@ process { withName: 'EDTA:CAT_CAT' { ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } } + + withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/raw/ltr" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/raw/tir" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } withName: 'EDTA:ANNOSINE' { ext.args = '--num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' @@ -20,6 +40,16 @@ process { ext.args = '-engine ncbi' } + withName: 'EDTA:REPEATMODELER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/raw/line" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { ext.args = '-pure_helitron' } @@ -40,34 +70,18 @@ process { } withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { - ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' + ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extout 0' } - withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } - - publishDir = [ - path: { "${params.outdir}/ltr" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } - - publishDir = [ - path: { "${params.outdir}/tir" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] + withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT_EXT' { + ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' } - withName: 'EDTA:REPEATMODELER_POSTPROCESS' { + withName: 'EDTA:HELITRONSCANNER_POSTPROCESS' { ext.prefix = { "${meta.id}.pp" } publishDir = [ - path: { "${params.outdir}/rm2" }, + path: { "${params.outdir}/raw/helitron" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/conf/test.config b/conf/test.config index 73fe0a6..29ab554 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,11 +1,11 @@ process { resourceLimits = [ - cpus: 4, - memory: '15.GB', + cpus: 10, + memory: '32.GB', time: '1.h' ] } params { - genome = 'https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa' + genome = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz' } \ No newline at end of file diff --git a/modules/local/helitronscanner_postprocess/environment.yml b/modules/local/helitronscanner_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/helitronscanner_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/helitronscanner_postprocess/main.nf b/modules/local/helitronscanner_postprocess/main.nf new file mode 100644 index 0000000..d0eb6a3 --- /dev/null +++ b/modules/local/helitronscanner_postprocess/main.nf @@ -0,0 +1,82 @@ +process HELITRONSCANNER_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/genome.HelitronScanner.filtered.fa" + path "input/genome.HelitronScanner.filtered.ext.fa" + + output: + tuple val(meta), path('*.Helitron.intact.raw.fa.anno.list') , emit: anno_list + tuple val(meta), path('*.Helitron.intact.raw.bed') , emit: raw_bed + tuple val(meta), path('*.Helitron.intact.raw.gff3') , emit: raw_gff + tuple val(meta), path('*.Helitron.intact.raw.fa') , emit: raw_fa + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_HelitronScanner_postprocess.sh \\ + $task.cpus + + cd input + + perl HelitronScanner_postprocess.pl + + cd - + + mv \\ + genome.Helitron.intact.raw.fa.anno.list \\ + ${prefix}.Helitron.intact.raw.fa.anno.list + + mv \\ + genome.Helitron.intact.raw.bed \\ + ${prefix}.Helitron.intact.raw.bed + + mv \\ + genome.Helitron.intact.raw.gff3 \\ + ${prefix}.Helitron.intact.raw.gff3 + + mv \\ + genome.Helitron.intact.raw.fa \\ + ${prefix}.Helitron.intact.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.Helitron.intact.raw.fa.anno.list + touch ${prefix}.Helitron.intact.raw.bed + touch ${prefix}.Helitron.intact.raw.gff3 + touch ${prefix}.Helitron.intact.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/utils/main.nf b/modules/local/utils/main.nf index fee91f3..dea2b26 100644 --- a/modules/local/utils/main.nf +++ b/modules/local/utils/main.nf @@ -41,4 +41,25 @@ def workflowVersionToYAML() { // def softwareVersionsToYAML(ch_versions) { return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) -} \ No newline at end of file +} + +// +// Gen a working sample ID from a file name +// +def idFromFileName(fileName) { + + def trial = ( fileName + ).replaceFirst( + /\.f(ast)?q$/, '' + ).replaceFirst( + /\.f(asta|sa|a|as|aa|na)?$/, '' + ).replaceFirst( + /\.gff(3)?$/, '' + ).replaceFirst( + /\.gz$/, '' + ) + + if ( trial == fileName ) { return fileName } + + return idFromFileName ( trial ) +} diff --git a/nextflow.config b/nextflow.config index 7eb1232..655993a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -51,8 +51,8 @@ process { process { resourceLimits = [ cpus: 12, - memory: '16.GB', - time: '1.hour' + memory: '72.GB', + time: '7.days' ] } @@ -95,9 +95,9 @@ conda { } manifest { - name = 'jguhlin/EDTA' + name = 'oushujun/EDTA' description = 'Extensive de-novo TE Annotator on Nextflow' - author = 'Usman Rashid, Joseph Guhlin & Shujun Ou' + author = 'Shujun Ou, Usman Rashid & Joseph Guhlin' version = '0.1.0dev' nextflowVersion = '!>=23.04.0' } diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index 5e111fb..d0cd760 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -19,12 +19,15 @@ nextflow_pipeline { false, [ 'pipeline_info/*.{html,json,txt,yml}', - 'ltr/*.pp.LTR.intact.raw.gff3', - 'ltr/*.pp.LTR.raw.fa', - 'tir/*.pp.TIR.intact.raw.fa', - 'tir/*.pp.TIR.intact.raw.gff3', - 'rm2/*.pp.LINE.raw.fa', - 'rm2/*.pp.RM2.fa', + 'raw/ltr/*.pp.LTR.intact.raw.gff3', + 'raw/ltr/*.pp.LTR.raw.fa', + 'raw/tir/*.pp.TIR.intact.raw.fa', + 'raw/tir/*.pp.TIR.intact.raw.gff3', + 'raw/line/*.pp.LINE.raw.fa', + 'raw/line/*.pp.RM2.fa', + 'raw/helitron/*.Helitron.intact.raw.fa', + 'raw/helitron/*.Helitron.intact.raw.fa.anno.list', + 'raw/helitron/*.Helitron.intact.raw.gff3' ], null, ['**'] diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index 636069c..e13891a 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 19, + "successful tasks": 21, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -13,12 +13,21 @@ "FORMAT_HELITRONSCANNER_OUT": { "perl": "v5.32.1" }, + "FORMAT_HELITRONSCANNER_OUT_EXT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, "HELITRONSCANNER_DRAW_RC": { "helitronscanner": "V1.1" }, + "HELITRONSCANNER_POSTPROCESS": { + "perl": "v5.32.1", + "trf": 4.09, + "TEsorter": "1.4.7", + "mdust": "2006.10.17" + }, "HELITRONSCANNER_SCAN_HEAD": { "helitronscanner": "V1.1" }, @@ -70,28 +79,35 @@ "mdust": "2006.10.17" }, "Workflow": { - "jguhlin/EDTA": "v0.1.0dev" + "oushujun/EDTA": "v0.1.0dev" } }, "stable paths": [ + "genome.pp.Helitron.intact.raw.bed:md5,a8b170a1ee8d36c7f8e3af5ba1e43cb6", "genome.pp.LTR.intact.raw.fa.anno.list:md5,51261f020350b448acdf89d8fb625448", "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25", "genome.pp.TIR.intact.raw.bed:md5,12406184046b11edc2ddadbc82765966" ], "stable names": [ - "ltr", - "ltr/genome.pp.LTR.intact.raw.fa.anno.list", - "ltr/genome.pp.LTR.intact.raw.gff3", - "ltr/genome.pp.LTR.raw.fa", - "ltr/genome.pp.genome.LTR.intact.raw.fa", "pipeline_info", - "rm2", - "rm2/genome.pp.LINE.raw.fa", - "rm2/genome.pp.RM2.fa", - "tir", - "tir/genome.pp.TIR.intact.raw.bed", - "tir/genome.pp.TIR.intact.raw.fa", - "tir/genome.pp.TIR.intact.raw.gff3" + "raw", + "raw/helitron", + "raw/helitron/genome.pp.Helitron.intact.raw.bed", + "raw/helitron/genome.pp.Helitron.intact.raw.fa", + "raw/helitron/genome.pp.Helitron.intact.raw.fa.anno.list", + "raw/helitron/genome.pp.Helitron.intact.raw.gff3", + "raw/line", + "raw/line/genome.pp.LINE.raw.fa", + "raw/line/genome.pp.RM2.fa", + "raw/ltr", + "raw/ltr/genome.pp.LTR.intact.raw.fa.anno.list", + "raw/ltr/genome.pp.LTR.intact.raw.gff3", + "raw/ltr/genome.pp.LTR.raw.fa", + "raw/ltr/genome.pp.genome.LTR.intact.raw.fa", + "raw/tir", + "raw/tir/genome.pp.TIR.intact.raw.bed", + "raw/tir/genome.pp.TIR.intact.raw.fa", + "raw/tir/genome.pp.TIR.intact.raw.gff3" ] } ], @@ -99,6 +115,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-12T18:08:43.061775" + "timestamp": "2024-12-13T11:02:40.702113" } } \ No newline at end of file diff --git a/tests/nf-test/tiny/main.nf.test.snap b/tests/nf-test/tiny/main.nf.test.snap index 20a57ef..896e0b8 100644 --- a/tests/nf-test/tiny/main.nf.test.snap +++ b/tests/nf-test/tiny/main.nf.test.snap @@ -2,7 +2,7 @@ "tiny genome": { "content": [ { - "successful tasks": 14, + "successful tasks": 15, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -13,6 +13,9 @@ "FORMAT_HELITRONSCANNER_OUT": { "perl": "v5.32.1" }, + "FORMAT_HELITRONSCANNER_OUT_EXT": { + "perl": "v5.32.1" + }, "HELITRONSCANNER_DRAW": { "helitronscanner": "V1.1" }, @@ -46,7 +49,7 @@ "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" }, "Workflow": { - "jguhlin/EDTA": "v0.1.0dev" + "oushujun/EDTA": "v0.1.0dev" } }, "stable paths": [ @@ -55,9 +58,9 @@ } ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-03T14:16:25.986375" + "timestamp": "2024-12-13T09:54:27.064885" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index ea91e2e..686b50d 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -1,68 +1,76 @@ -include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' -include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' -include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' -include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' -include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' -include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' -include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' -include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main.nf' -include { REPEATMODELER_POSTPROCESS } from '../modules/local/repeatmodeler_postprocess/main.nf' - -include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' + +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' +include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' + +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' +include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main.nf' + +include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' + +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' +include { REPEATMODELER_POSTPROCESS } from '../modules/local/repeatmodeler_postprocess/main.nf' + +include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' +include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' +include { FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT } from '../modules/local/format_helitronscanner_out/main.nf' +include { HELITRONSCANNER_POSTPROCESS } from '../modules/local/helitronscanner_postprocess/main.nf' + + + +include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' +include { idFromFileName } from '../modules/local/utils/main.nf' workflow EDTA { main: // Versions channel - ch_versions = Channel.empty() + ch_versions = Channel.empty() - ch_genome = Channel.fromPath(params.genome) - - // Create a meta object for each genome - ch_meta_genome = ch_genome.map { genome -> - def meta = [:] - meta.id = genome.baseName - - [ meta, genome ] - } + ch_genome = Channel.fromPath(params.genome) + | map { genome -> + def meta = [:] + meta.id = idFromFileName ( genome.baseName ) + + [ meta, genome ] + } // MODULE: SANITIZE_HEADERS - SANITIZE_HEADERS ( ch_meta_genome ) + SANITIZE_HEADERS ( ch_genome ) - ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta + ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta // MODULE: LTRHARVEST LTRHARVEST ( ch_sanitized_fasta ) - ch_ltrharvest_scn = LTRHARVEST.out.scn + ch_ltrharvest_scn = LTRHARVEST.out.scn - ch_versions = ch_versions.mix(LTRHARVEST.out.versions) + ch_versions = ch_versions.mix(LTRHARVEST.out.versions) // MODULE: LTRFINDER LTRFINDER { ch_sanitized_fasta } - ch_ltrfinder_scn = LTRFINDER.out.scn + ch_ltrfinder_scn = LTRFINDER.out.scn - ch_versions = ch_versions.mix(LTRFINDER.out.versions) + ch_versions = ch_versions.mix(LTRFINDER.out.versions) // MODULE: CAT_CAT - ch_cat_cat_inputs = ch_ltrharvest_scn - | join(ch_ltrfinder_scn) - | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } + ch_cat_cat_inputs = ch_ltrharvest_scn + | join(ch_ltrfinder_scn) + | map { meta, harvested, found -> [ meta, [ harvested, found ] ] } CAT_CAT ( ch_cat_cat_inputs ) - ch_ltr_candidates = CAT_CAT.out.file_out - ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) + ch_ltr_candidates = CAT_CAT.out.file_out + ch_versions = ch_versions.mix(CAT_CAT.out.versions.first()) // MODULE: LTRRETRIEVER_LTRRETRIEVER - ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) + ch_ltrretriever_inputs = ch_sanitized_fasta.join(ch_ltr_candidates) LTRRETRIEVER_LTRRETRIEVER ( ch_ltrretriever_inputs.map { meta, fasta, _ltr -> [ meta, fasta ] }, @@ -72,12 +80,33 @@ workflow EDTA { [] ) - ch_pass_list = LTRRETRIEVER_LTRRETRIEVER.out.pass_list - ch_pass_list_gff = LTRRETRIEVER_LTRRETRIEVER.out.pass_list_gff - ch_annotation_gff = LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff - ch_defalse = LTRRETRIEVER_LTRRETRIEVER.out.defalse - ch_ltrlib = LTRRETRIEVER_LTRRETRIEVER.out.ltrlib - ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) + ch_versions = ch_versions.mix(LTRRETRIEVER_LTRRETRIEVER.out.versions.first()) + + // MODULE: LTR_RETRIEVER_POSTPROCESS + ch_ltr_retriever_postprocess_inputs = ch_sanitized_fasta + | join ( LTRRETRIEVER_LTRRETRIEVER.out.pass_list ) + | join ( LTRRETRIEVER_LTRRETRIEVER.out.pass_list_gff ) + | join ( LTRRETRIEVER_LTRRETRIEVER.out.annotation_gff ) + | join ( LTRRETRIEVER_LTRRETRIEVER.out.defalse ) + | join ( LTRRETRIEVER_LTRRETRIEVER.out.ltrlib ) + | multiMap { meta, fasta, pass, p_gff, a_gff, defalse, ltr -> + genome: [ meta, fasta ] + pass : pass + p_gff : p_gff + a_gff : a_gff + defalse : defalse + ltr : ltr + } + + LTR_RETRIEVER_POSTPROCESS ( + ch_ltr_retriever_postprocess_inputs.genome, + ch_ltr_retriever_postprocess_inputs.pass, + ch_ltr_retriever_postprocess_inputs.p_gff, + ch_ltr_retriever_postprocess_inputs.defalse, + ch_ltr_retriever_postprocess_inputs.ltr, + ) + + ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) // MODULE: TIRLEARNER TIRLEARNER ( @@ -85,11 +114,25 @@ workflow EDTA { params.species ) - ch_tirlearner_fasta = TIRLEARNER.out.fasta - ch_tirlearner_gff = TIRLEARNER.out.gff - ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + + // MODULE: TIR_LEARNER_POSTPROCESS + ch_tir_learner_postprocess_inputs = ch_sanitized_fasta + | join ( TIRLEARNER.out.fasta ) + | join ( TIRLEARNER.out.gff ) + | multiMap { meta, fasta, tir_fa, tir_gff -> + genome : [ meta, fasta ] + tir_fa : tir_fa + tir_gff : tir_gff + } + TIR_LEARNER_POSTPROCESS ( + ch_tir_learner_postprocess_inputs.genome, + ch_tir_learner_postprocess_inputs.tir_fa, + ch_tir_learner_postprocess_inputs.tir_gff + ) + + ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) - // These can also run in parallel // MODULE: ANNOSINE ANNOSINE ( ch_sanitized_fasta, @@ -97,55 +140,64 @@ workflow EDTA { ) // Currently it's a topic, so need to fix that - ch_versions = ch_versions.mix(ANNOSINE.out.versions) - cb_annosine_seed_sine = ANNOSINE.out.fa + ch_versions = ch_versions.mix(ANNOSINE.out.versions) + ch_annosine_seed_sine = ANNOSINE.out.fa // MODULE: REPEATMODELER_BUILDDATABASE - ch_repeatmodeler_inputs = ch_sanitized_fasta - | map { meta, fasta -> - def size = fasta.size() - def size_threshold = 100_000 // bytes -> bp - - // TODO: Not the best way to set a size threshold - // but it is simple - // This is needed to avoid, - // Error: Database genome is not large enough ( minimum 40000 bp ) to process with RepeatModeler. - if ( size < size_threshold ) { - log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" - return null - } - - return [ meta, fasta ] - } - | filter { it } + ch_repeatmodeler_inputs = ch_sanitized_fasta + | map { meta, fasta -> + def size = fasta.size() + def size_threshold = 100_000 // bytes -> bp + + if ( size < size_threshold ) { + log.warn "RepeatModeler is skipped for genome '${meta.id}' as it is smaller than ${size_threshold} bytes" + return null + } + + return [ meta, fasta ] + } + | filter { it } REPEATMODELER_BUILDDATABASE ( ch_repeatmodeler_inputs ) - ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db - ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) + ch_repeatmodeler_db = REPEATMODELER_BUILDDATABASE.out.db + ch_versions = ch_versions.mix(REPEATMODELER_BUILDDATABASE.out.versions.first()) // MODULE: REPEATMODELER_REPEATMODELER REPEATMODELER_REPEATMODELER ( ch_repeatmodeler_db ) - ch_repeatmodeler_fasta = REPEATMODELER_REPEATMODELER.out.fasta - ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + ch_versions = ch_versions.mix(REPEATMODELER_REPEATMODELER.out.versions.first()) + + // MODULE: REPEATMODELER_POSTPROCESS + ch_repeatmodeler_postprocess_inputs = ch_sanitized_fasta + | join ( REPEATMODELER_REPEATMODELER.out.fasta ) + | multiMap { meta, fasta, rm_fa -> + genome : [ meta, fasta ] + rm_fa : rm_fa + } + REPEATMODELER_POSTPROCESS ( + ch_repeatmodeler_postprocess_inputs.genome, + ch_repeatmodeler_postprocess_inputs.rm_fa, + ) + + ch_versions = ch_versions.mix(REPEATMODELER_POSTPROCESS.out.versions.first()) // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) - ch_helitronscanner_draw = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw - ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc - ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) + ch_helitronscanner_draw = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw + ch_helitronscanner_draw_rc = FASTA_HELITRONSCANNER_SCAN_DRAW.out.helitronscanner_draw_rc + ch_versions = ch_versions.mix(FASTA_HELITRONSCANNER_SCAN_DRAW.out.versions) // MODULE: FORMAT_HELITRONSCANNER_OUT - ch_format_helitronscanner_inputs = ch_sanitized_fasta - | join(ch_helitronscanner_draw) - | join(ch_helitronscanner_draw_rc) - | multiMap { meta, fasta, draw, draw_rc -> - genome: [ meta, fasta ] - hel_fa: draw - rc_hel_fa: draw_rc - } + ch_format_helitronscanner_inputs = ch_sanitized_fasta + | join(ch_helitronscanner_draw) + | join(ch_helitronscanner_draw_rc) + | multiMap { meta, fasta, draw, draw_rc -> + genome: [ meta, fasta ] + hel_fa: draw + rc_hel_fa: draw_rc + } FORMAT_HELITRONSCANNER_OUT ( ch_format_helitronscanner_inputs.genome, @@ -153,82 +205,56 @@ workflow EDTA { ch_format_helitronscanner_inputs.rc_hel_fa, ) - ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) - - // MODULE: LTR_RETRIEVER_POSTPROCESS - ch_ltr_retriever_postprocess_inputs = ch_sanitized_fasta - | join(ch_pass_list) - | join(ch_pass_list_gff) - | join(ch_annotation_gff) - | join(ch_defalse) - | join(ch_ltrlib) - | multiMap { meta, fasta, pass, p_gff, a_gff, defalse, ltr -> - genome: [ meta, fasta ] - pass : pass - p_gff : p_gff - a_gff : a_gff - defalse : defalse - ltr : ltr - } + ch_helitronscanner_out_fa = FORMAT_HELITRONSCANNER_OUT.out.filtered_fa + | filter { _meta, fasta -> fasta.countFasta() > 0 } + ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT.out.versions.first()) - LTR_RETRIEVER_POSTPROCESS ( - ch_ltr_retriever_postprocess_inputs.genome, - ch_ltr_retriever_postprocess_inputs.pass, - ch_ltr_retriever_postprocess_inputs.p_gff, - ch_ltr_retriever_postprocess_inputs.defalse, - ch_ltr_retriever_postprocess_inputs.ltr, - ) - - ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) - - // MODULE: TIR_LEARNER_POSTPROCESS - ch_tir_learner_postprocess_inputs = ch_sanitized_fasta - | join(ch_tirlearner_fasta) - | join(ch_tirlearner_gff) - | multiMap { meta, fasta, tir_fa, tir_gff -> - genome : [ meta, fasta ] - tir_fa : tir_fa - tir_gff : tir_gff - } - TIR_LEARNER_POSTPROCESS ( - ch_tir_learner_postprocess_inputs.genome, - ch_tir_learner_postprocess_inputs.tir_fa, - ch_tir_learner_postprocess_inputs.tir_gff + + // MODULE: FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT + FORMAT_HELITRONSCANNER_OUT_EXT ( + ch_format_helitronscanner_inputs.genome, + ch_format_helitronscanner_inputs.hel_fa, + ch_format_helitronscanner_inputs.rc_hel_fa, ) - ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) - - // MODULE: REPEATMODELER_POSTPROCESS - ch_repeatmodeler_postprocess_inputs = ch_sanitized_fasta - | join(ch_repeatmodeler_fasta) - | multiMap { meta, fasta, rm_fa -> - genome : [ meta, fasta ] - rm_fa : rm_fa - } - REPEATMODELER_POSTPROCESS ( - ch_repeatmodeler_postprocess_inputs.genome, - ch_repeatmodeler_postprocess_inputs.rm_fa, + ch_helitronscanner_out_ext_fa = FORMAT_HELITRONSCANNER_OUT_EXT.out.filtered_ext_fa + | filter { _meta, fasta -> fasta.countFasta() > 0 } + ch_versions = ch_versions.mix(FORMAT_HELITRONSCANNER_OUT_EXT.out.versions.first()) + + // MODULE: HELITRONSCANNER_POSTPROCESS + ch_helitronscanner_post_inputs = ch_sanitized_fasta + | join(ch_helitronscanner_out_fa) + | join(ch_helitronscanner_out_ext_fa) + | multiMap { meta, fasta, hs_fa, hs_ext_fa -> + genome : [ meta, fasta ] + hs_fa : hs_fa + hs_ext_fa : hs_ext_fa + } + HELITRONSCANNER_POSTPROCESS ( + ch_helitronscanner_post_inputs.genome, + ch_helitronscanner_post_inputs.hs_fa, + ch_helitronscanner_post_inputs.hs_ext_fa, ) - ch_versions = ch_versions.mix(REPEATMODELER_POSTPROCESS.out.versions.first()) + ch_versions = ch_versions.mix(HELITRONSCANNER_POSTPROCESS.out.versions.first()) // Function: Save versions - ch_versions = ch_versions - | unique - | map { yml -> - if ( yml ) { yml } - } + ch_versions = ch_versions + | unique + | map { yml -> + if ( yml ) { yml } + } - ch_versions_yml = softwareVersionsToYAML(ch_versions) - | collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'software_versions.yml', - sort: true, - newLine: true, - cache: false - ) + ch_versions_yml = softwareVersionsToYAML(ch_versions) + | collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'software_versions.yml', + sort: true, + newLine: true, + cache: false + ) emit: - versions_yml = ch_versions_yml // [ software_versions.yml ] + versions_yml = ch_versions_yml // [ software_versions.yml ] } \ No newline at end of file From 81207b36ca46a0fc5b53584f8bd4ba7c16a5f915 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 13 Dec 2024 12:19:32 +1300 Subject: [PATCH 38/49] Added ANNOSINE_POSTPROCESS --- bin/setup_AnnoSINE_postprocess.sh | 18 +++ conf/modules.config | 22 +++- conf/test.config | 12 +- main.nf | 4 - .../annosine_postprocess/environment.yml | 10 ++ modules/local/annosine_postprocess/main.nf | 63 +++++++++++ nextflow.config | 8 +- workflows/edta.nf | 107 ++++++++++-------- 8 files changed, 181 insertions(+), 63 deletions(-) create mode 100755 bin/setup_AnnoSINE_postprocess.sh create mode 100644 modules/local/annosine_postprocess/environment.yml create mode 100644 modules/local/annosine_postprocess/main.nf diff --git a/bin/setup_AnnoSINE_postprocess.sh b/bin/setup_AnnoSINE_postprocess.sh new file mode 100755 index 0000000..daf76fe --- /dev/null +++ b/bin/setup_AnnoSINE_postprocess.sh @@ -0,0 +1,18 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > input/AnnoSINE_postprocess.pl << EOF +my \$genome = 'genome'; +my \$threads = $1; + +my \$cleanup_misclas = '$script_path/cleanup_misclas.pl'; +my \$cleanup_tandem = '$script_path/cleanup_tandem.pl'; + +my \$TEsorter = ''; # Assumed on PATH +my \$trf = '$(which trf)'; + +EOF + +sed -n 490,497p "$script_path/EDTA_raw.pl" \ + >> input/AnnoSINE_postprocess.pl diff --git a/conf/modules.config b/conf/modules.config index ff251a2..9482021 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,19 +22,19 @@ process { ] } - withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { + withName: 'EDTA:ANNOSINE' { + ext.args = params.annosine_ext_args ?: '-a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' + } + + withName: 'EDTA:ANNOSINE_POSTPROCESS' { ext.prefix = { "${meta.id}.pp" } publishDir = [ - path: { "${params.outdir}/raw/tir" }, + path: { "${params.outdir}/raw/sine" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - - withName: 'EDTA:ANNOSINE' { - ext.args = '--num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' - } withName: 'EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' @@ -50,6 +50,16 @@ process { ] } + withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { + ext.prefix = { "${meta.id}.pp" } + + publishDir = [ + path: { "${params.outdir}/raw/tir" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { ext.args = '-pure_helitron' } diff --git a/conf/test.config b/conf/test.config index 29ab554..7f76e47 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,3 +1,11 @@ +params { + genome = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz' + + // Following parameters for ANNOSINE are not recommended. + // These are used here with the test data to produce testable outputs + annosine_ext_args = '-a 2 -rpm 0 --copy_number 1 --shift 200' +} + process { resourceLimits = [ cpus: 10, @@ -5,7 +13,3 @@ process { time: '1.h' ] } - -params { - genome = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz' -} \ No newline at end of file diff --git a/main.nf b/main.nf index 6607f9e..a50616d 100755 --- a/main.nf +++ b/main.nf @@ -2,10 +2,6 @@ nextflow.enable.dsl = 2 -params.genome = 'genomes/*' -params.species = 'others' -params.outdir = 'results' - include { EDTA } from './workflows/edta.nf' workflow { diff --git a/modules/local/annosine_postprocess/environment.yml b/modules/local/annosine_postprocess/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/annosine_postprocess/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/annosine_postprocess/main.nf b/modules/local/annosine_postprocess/main.nf new file mode 100644 index 0000000..42814ca --- /dev/null +++ b/modules/local/annosine_postprocess/main.nf @@ -0,0 +1,63 @@ +process ANNOSINE_POSTPROCESS { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'input/genome') + path "input/Seed_SINE.fa" + + output: + tuple val(meta), path('*.SINE.raw.fa') , emit: sine_fa + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + setup_AnnoSINE_postprocess.sh \\ + $task.cpus + + cd input + + perl AnnoSINE_postprocess.pl + + cd - + + mv \\ + input/genome.SINE.raw.fa \\ + ${prefix}.SINE.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.SINE.raw.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + trf: \$(trf -v |& sed -n 's|.*Version \\(.*\\)|\\1|p') + TEsorter: \$(TEsorter -v | tr -d 'TEsorter ') + mdust: $MDUST_VERSION + END_VERSIONS + """ +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 655993a..25a0b75 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,5 +1,11 @@ params { - publish_dir_mode = 'copy' + genome = 'genomes/*' + species = 'others' + outdir = 'results' + + annosine_ext_args = null + + publish_dir_mode = 'copy' } process { diff --git a/workflows/edta.nf b/workflows/edta.nf index 686b50d..9d23a07 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -1,29 +1,28 @@ -include { SANITIZE_HEADERS } from '../modules/local/sanitize/main.nf' +include { SANITIZE_HEADERS } from '../modules/local/sanitize/main' -include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main.nf' -include { LTRFINDER } from '../modules/nf-core/ltrfinder/main.nf' -include { CAT_CAT } from '../modules/nf-core/cat/cat/main.nf' -include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main.nf' -include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main.nf' +include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main' +include { LTRFINDER } from '../modules/nf-core/ltrfinder/main' +include { CAT_CAT } from '../modules/nf-core/cat/cat/main' +include { LTRRETRIEVER_LTRRETRIEVER } from '../modules/nf-core/ltrretriever/ltrretriever/main' +include { LTR_RETRIEVER_POSTPROCESS } from '../modules/local/ltr_retriever_postprocess/main' -include { TIRLEARNER } from '../modules/gallvp/tirlearner/main.nf' -include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main.nf' +include { ANNOSINE } from '../modules/gallvp/annosine/main' +include { ANNOSINE_POSTPROCESS } from '../modules/local/annosine_postprocess/main' -include { ANNOSINE } from '../modules/gallvp/annosine/main.nf' +include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main' +include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main' +include { REPEATMODELER_POSTPROCESS } from '../modules/local/repeatmodeler_postprocess/main' -include { REPEATMODELER_BUILDDATABASE } from '../modules/nf-core/repeatmodeler/builddatabase/main.nf' -include { REPEATMODELER_REPEATMODELER } from '../modules/nf-core/repeatmodeler/repeatmodeler/main.nf' -include { REPEATMODELER_POSTPROCESS } from '../modules/local/repeatmodeler_postprocess/main.nf' +include { TIRLEARNER } from '../modules/gallvp/tirlearner/main' +include { TIR_LEARNER_POSTPROCESS } from '../modules/local/tir_learner_postprocess/main' -include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main.nf' -include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main.nf' -include { FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT } from '../modules/local/format_helitronscanner_out/main.nf' -include { HELITRONSCANNER_POSTPROCESS } from '../modules/local/helitronscanner_postprocess/main.nf' +include { FASTA_HELITRONSCANNER_SCAN_DRAW } from '../subworkflows/gallvp/fasta_helitronscanner_scan_draw/main' +include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/format_helitronscanner_out/main' +include { FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT } from '../modules/local/format_helitronscanner_out/main' +include { HELITRONSCANNER_POSTPROCESS } from '../modules/local/helitronscanner_postprocess/main' - - -include { softwareVersionsToYAML } from '../modules/local/utils/main.nf' -include { idFromFileName } from '../modules/local/utils/main.nf' +include { softwareVersionsToYAML } from '../modules/local/utils/main' +include { idFromFileName } from '../modules/local/utils/main' workflow EDTA { @@ -51,14 +50,14 @@ workflow EDTA { ch_ltrharvest_scn = LTRHARVEST.out.scn - ch_versions = ch_versions.mix(LTRHARVEST.out.versions) + ch_versions = ch_versions.mix(LTRHARVEST.out.versions.first()) // MODULE: LTRFINDER LTRFINDER { ch_sanitized_fasta } ch_ltrfinder_scn = LTRFINDER.out.scn - ch_versions = ch_versions.mix(LTRFINDER.out.versions) + ch_versions = ch_versions.mix(LTRFINDER.out.versions.first()) // MODULE: CAT_CAT ch_cat_cat_inputs = ch_ltrharvest_scn @@ -108,40 +107,27 @@ workflow EDTA { ch_versions = ch_versions.mix(LTR_RETRIEVER_POSTPROCESS.out.versions.first()) - // MODULE: TIRLEARNER - TIRLEARNER ( + // MODULE: ANNOSINE + ANNOSINE ( ch_sanitized_fasta, - params.species + 3 // mode ) - ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + ch_versions = ch_versions.mix(ANNOSINE.out.versions.first()) - // MODULE: TIR_LEARNER_POSTPROCESS - ch_tir_learner_postprocess_inputs = ch_sanitized_fasta - | join ( TIRLEARNER.out.fasta ) - | join ( TIRLEARNER.out.gff ) - | multiMap { meta, fasta, tir_fa, tir_gff -> + // MODULE: ANNOSINE_POSTPROCESS + ch_annosine_postprocess_inputs = ch_sanitized_fasta + | join ( ANNOSINE.out.fa ) + | multiMap { meta, fasta, anno_fa -> genome : [ meta, fasta ] - tir_fa : tir_fa - tir_gff : tir_gff + anno_fa : anno_fa } - TIR_LEARNER_POSTPROCESS ( - ch_tir_learner_postprocess_inputs.genome, - ch_tir_learner_postprocess_inputs.tir_fa, - ch_tir_learner_postprocess_inputs.tir_gff + ANNOSINE_POSTPROCESS ( + ch_annosine_postprocess_inputs.genome, + ch_annosine_postprocess_inputs.anno_fa ) - ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) - - // MODULE: ANNOSINE - ANNOSINE ( - ch_sanitized_fasta, - 3 // mode - ) - - // Currently it's a topic, so need to fix that - ch_versions = ch_versions.mix(ANNOSINE.out.versions) - ch_annosine_seed_sine = ANNOSINE.out.fa + ch_versions = ch_versions.mix(ANNOSINE_POSTPROCESS.out.versions.first()) // MODULE: REPEATMODELER_BUILDDATABASE ch_repeatmodeler_inputs = ch_sanitized_fasta @@ -182,6 +168,31 @@ workflow EDTA { ch_versions = ch_versions.mix(REPEATMODELER_POSTPROCESS.out.versions.first()) + // MODULE: TIRLEARNER + TIRLEARNER ( + ch_sanitized_fasta, + params.species + ) + + ch_versions = ch_versions.mix(TIRLEARNER.out.versions.first()) + + // MODULE: TIR_LEARNER_POSTPROCESS + ch_tir_learner_postprocess_inputs = ch_sanitized_fasta + | join ( TIRLEARNER.out.fasta ) + | join ( TIRLEARNER.out.gff ) + | multiMap { meta, fasta, tir_fa, tir_gff -> + genome : [ meta, fasta ] + tir_fa : tir_fa + tir_gff : tir_gff + } + TIR_LEARNER_POSTPROCESS ( + ch_tir_learner_postprocess_inputs.genome, + ch_tir_learner_postprocess_inputs.tir_fa, + ch_tir_learner_postprocess_inputs.tir_gff + ) + + ch_versions = ch_versions.mix(TIR_LEARNER_POSTPROCESS.out.versions.first()) + // MODULE: FASTA_HELITRONSCANNER_SCAN_DRAW FASTA_HELITRONSCANNER_SCAN_DRAW ( ch_sanitized_fasta ) From ba29b092faab91373370454f364b0969b9881c39 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 13 Dec 2024 15:50:43 +1300 Subject: [PATCH 39/49] Added PROCESS_K --- .github/check_binaries.sh | 9 + bin/EDTA_processK.pl | 216 ++++++++++++++++++ conf/modules.config | 10 + modules/local/process_k/environment.yml | 8 + modules/local/process_k/main.nf | 89 ++++++++ .../local/repeatmodeler_postprocess/main.nf | 13 +- tests/nf-test/small/main.nf.test | 3 +- tests/nf-test/small/main.nf.test.snap | 14 +- workflows/edta.nf | 45 ++++ 9 files changed, 397 insertions(+), 10 deletions(-) create mode 100755 bin/EDTA_processK.pl create mode 100644 modules/local/process_k/environment.yml create mode 100644 modules/local/process_k/main.nf diff --git a/.github/check_binaries.sh b/.github/check_binaries.sh index 79e8784..354d472 100755 --- a/.github/check_binaries.sh +++ b/.github/check_binaries.sh @@ -10,3 +10,12 @@ if [[ $EDTA_raw_pl_version != $bin_EDTA_raw_pl_version ]]; then echo 'Please synchronize bin/EDTA_raw.pl with EDTA_raw.pl' exit 1 fi + +EDTA_processK_pl_version=$(md5sum EDTA_processK.pl | cut -f1 -d' ') +bin_EDTA_processK_pl_version=$(md5sum bin/EDTA_processK.pl | cut -f1 -d' ') + +if [[ $EDTA_processK_pl_version != $bin_EDTA_processK_pl_version ]]; then + echo 'EDTA_processK.pl != bin/EDTA_processK.pl' + echo 'Please synchronize bin/EDTA_processK.pl with EDTA_processK.pl' + exit 1 +fi diff --git a/bin/EDTA_processK.pl b/bin/EDTA_processK.pl new file mode 100755 index 0000000..002e43f --- /dev/null +++ b/bin/EDTA_processK.pl @@ -0,0 +1,216 @@ +#!/usr/bin/env perl +use warnings; +use strict; +use FindBin; +use File::Basename; + +##################################################################### +##### Perform EDTA basic and advance filtering on TE candidates ##### +##### Shujun Ou (shujun.ou.1@gmail.com, 12/28/2023) ##### +##################################################################### + +## Input: +# $genome.SINE.raw.fa +# $genome.LINE.raw.fa +# $genome.LTR.raw.fa +# $genome.LTR.intact.raw.fa +# $genome.TIR.intact.raw.fa +# $genome.Helitron.intact.raw.fa + +## Output: +# $genome.EDTA.fa.stg1 + +my $usage = "\nPerform EDTA basic and advance filtering for raw TE candidates and generate the stage 1 library + perl EDTA_processF.pl [options] + -genome [File] The genome FASTA + -ltr [File] The raw LTR library FASTA + -ltrint [File] The intact LTR library FASTA + -sine [File] The raw SINE library FASTA + -line [File] The raw LINE library FASTA + -tir [File] The raw TIR library FASTA + -helitron [File] The raw Helitron library FASTA + -mindiff_ltr [float] The minimum fold difference in richness between LTRs and contaminants (default: 1) + -mindiff_tir [float] The minimum fold difference in richness between TIRs and contaminants (default: 1) + -mindiff_hel [float] The minimum fold difference in richness between Helitrons and contaminants (default: 2) + -repeatmasker [path] The directory containing RepeatMasker (default: read from ENV) + -blast [path] The directory containing Blastn (default: read from ENV) + -threads|-t [int] Number of theads to run this script + -help|-h Display this help info +\n"; + +# user input +my $genome = ''; +my $LTRraw = ''; +my $LTRintact = ''; +my $SINEraw = ''; +my $LINEraw = ''; +my $TIRraw = ''; +my $HELraw = ''; +my $err = ''; + +# minimum richness difference between $TE1 and $TE2 for a sequence to be considered as REAL to $TE1. +# Smaller number is more inclusive during purging, hence higher false positives +my $mindiff_LTR = 1; +my $mindiff_TIR = 1; +my $mindiff_HEL = 1.5; + +my $threads = 4; +my $script_path = $FindBin::Bin; +my $TE_purifier = "$script_path/bin/TE_purifier.pl"; +my $rename_TE = "$script_path/bin/rename_TE.pl"; +my $cleanup_tandem = "$script_path/bin/cleanup_tandem.pl"; +my $cleanup_nested = "$script_path/bin/cleanup_nested.pl"; +my $cleanup_proteins = "$script_path/bin/cleanup_proteins.pl"; +my $repeatmasker = " "; +my $blast = " "; + +# read parameters +my $k=0; +foreach (@ARGV){ + $genome = $ARGV[$k+1] if /^-genome$/i and $ARGV[$k+1] !~ /^-/; + $LTRraw = $ARGV[$k+1] if /^-ltr$/i and $ARGV[$k+1] !~ /^-/; + $LTRintact = $ARGV[$k+1] if /^-ltrint$/i and $ARGV[$k+1] !~ /^-/; + $SINEraw = $ARGV[$k+1] if /^-sine$/i and $ARGV[$k+1] !~ /^-/; + $LINEraw = $ARGV[$k+1] if /^-line$/i and $ARGV[$k+1] !~ /^-/; + $TIRraw = $ARGV[$k+1] if /^-tir/i and $ARGV[$k+1] !~ /^-/; + $HELraw = $ARGV[$k+1] if /^-helitron/i and $ARGV[$k+1] !~ /^-/; + $mindiff_LTR = $ARGV[$k+1] if /^-mindiff_ltr/i and $ARGV[$k+1] !~ /^-/; + $mindiff_TIR = $ARGV[$k+1] if /^-mindiff_tir/i and $ARGV[$k+1] !~ /^-/; + $mindiff_HEL = $ARGV[$k+1] if /^-mindiff_hel/i and $ARGV[$k+1] !~ /^-/; + $repeatmasker = $ARGV[$k+1] if /^-repeatmasker/i and $ARGV[$k+1] !~ /^-/; + $blast = $ARGV[$k+1] if /^-blast/i and $ARGV[$k+1] !~ /^-/; + $threads = $ARGV[$k+1] if /^-threads$|^-t$/i and $ARGV[$k+1] !~ /^-/; + die $usage if /^-help$|^-h$/i; + $k++; + } + +# check files and dependencies +die "Genome file $genome not exists!\n$usage" unless -s $genome; +die "LTR raw library file $LTRraw not exists!\n$usage" unless -s $LTRraw; +die "Intact LTR file $LTRintact not exists!\n$usage" unless -s $LTRintact; +#die "LINE raw library file $LINEraw not exists!\n$usage" unless -e $LINE; # allow empty file +#die "SINE raw library file $SINEraw not exists!\n$usage" unless -e $SINE; # allow empty file +die "TIR raw library file $TIRraw not exists!\n$usage" unless -s $TIRraw; +die "Helitron raw library file $HELraw not exists!\n$usage" unless -s $HELraw; +die "The script TE_purifier.pl is not found in $TE_purifier!\n" unless -s $TE_purifier; +die "The script rename_TE.pl is not found in $rename_TE!\n" unless -s $rename_TE; +die "The script cleanup_tandem.pl is not found in $cleanup_tandem!\n" unless -s $cleanup_tandem; +die "The script cleanup_nested.pl is not found in $cleanup_nested!\n" unless -s $cleanup_nested; +die "The script cleanup_proteins.pl is not found in $cleanup_proteins!\n" unless -s $cleanup_proteins; + +# make a softlink to the genome +my $genome_file = basename($genome); +`ln -s $genome $genome_file` unless -e $genome_file; +$genome = $genome_file; +my $LTR = "$genome.LTR.raw.fa"; +my $LTRint = "$genome.LTR.intact.raw.fa"; +my $SINE = "$genome.SINE.raw.fa"; +my $LINE = "$genome.LINE.raw.fa"; +my $TIR = "$genome.TIR.intact.raw.fa"; +my $HEL = "$genome.Helitron.intact.raw.fa"; + +# Make working directories +`mkdir $genome.EDTA.combine` unless -e "$genome.EDTA.combine" && -d "$genome.EDTA.combine"; + +# enter the combine folder for EDTA processing +chdir "$genome.EDTA.combine"; +`cp ../$LTRraw $LTR` unless -s "$LTR"; +`cp ../$LTRintact $LTRint` unless -s "$LTRint"; +`cp ../$SINEraw $SINE` unless -s "$SINE"; +`cp ../$LINEraw $LINE` unless -s "$LINE"; +`cp ../$TIRraw $TIR` unless -s "$TIR"; +`cp ../$HELraw $HEL` unless -s "$HEL"; + + +################################## +###### define subroutines ###### +################################## + +# purify $TE2 contaminants in $TE1 +# This function better works for redundant libraries +sub Purifier() { + my ($TE1, $TE2, $mindiff) = ($_[0], $_[1], $_[2]); + # mark contaminents with lowercase letters based on relative richness + `perl $TE_purifier -TE1 $TE1 -TE2 $TE2 -t $threads -mindiff $mindiff`; + # remove lowercase sequences + `perl $cleanup_tandem -misschar l -Nscreen 1 -nc 50000 -nr 0.8 -minlen 80 -cleanN 1 -cleanT 1 -minrm 1 -trf 0 -f $TE1-$TE2.fa > $TE1.HQ`; + } + + +################################# +###### Advance filtering ###### +################################# + +## Purge contaminants in redundant libraries +# purify raw LTR (clean LTR library is better than dirty intact LTR for purging LTRs from other TEs) +&Purifier("$LTR", "$TIR", $mindiff_LTR); +&Purifier("$LTR.HQ", "$HEL", $mindiff_LTR); +`mv $LTR.HQ.HQ $LTR.HQ`; + +# purify Helitron +&Purifier("$HEL", "$TIR", $mindiff_HEL); +&Purifier("$HEL.HQ", "$LTR", $mindiff_LTR); +`perl $cleanup_tandem -misschar l -Nscreen 1 -nc 50000 -nr 0.8 -minlen 80 -cleanN 1 -cleanT 0 -minrm 1 -trf 0 -f $HEL.HQ-$LTR.fa > $HEL.int.cln`; # more relaxed in filtering intact helitrons +`mv $HEL.HQ.HQ $HEL.cln`; + +# purify TIR +&Purifier("$TIR", "$LTR", $mindiff_TIR); +&Purifier("$TIR.HQ", "$HEL", $mindiff_TIR); +`perl $cleanup_tandem -misschar l -Nscreen 1 -nc 50000 -nr 0.8 -minlen 80 -cleanN 1 -cleanT 0 -minrm 1 -trf 0 -f $TIR.HQ-$HEL.fa > $TIR.int.cln`; # more relaxed in filtering intact TIRs +`mv $TIR.HQ.HQ $TIR.cln`; + +# purify intact LTR from TIRs. Including Helitron is too damaging for now. +&Purifier("$LTRint", "$TIR.cln", 10); # 10 is permissive +`perl $cleanup_tandem -misschar l -Nscreen 1 -nc 50000 -nr 0.8 -minlen 80 -cleanN 1 -cleanT 0 -minrm 1 -trf 0 -f $LTRint-$TIR.cln.fa > $LTRint.cln`; +#&Purifier("$LTRint.HQ", "$HEL.cln", 10); # 10 is permissive +#`perl $cleanup_tandem -misschar l -Nscreen 1 -nc 50000 -nr 0.8 -minlen 80 -cleanN 1 -cleanT 0 -minrm 1 -trf 0 -f $LTRint.HQ-$HEL.cln.fa > $LTRint.cln`; # more relaxed in filtering intact LTRs + +## Purge contaminants in non-redundant libraries +# clean LINEs in LTRs +if (-s "$LINE"){ + $err = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -nolow -div 40 -lib $LINE $LTR 2>&1`; + if ($err !~ /done/) { + `ln -s $LTR $LTR.masked` if $err =~ s/^.*(No repetitive sequences were detected.*)\s+$/Warning: No sequences were masked/s; + print STDERR "\n$err\n"; + } + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 80 -minscore 3000 -trf 0 -cleanN 1 -cleanT 1 -f $LTR.masked > $LTR.cln`; + } else { + `cp $LTR $LTR.cln`; + } + +# clean LINEs and LTRs in SINEs +if (-s "$SINE"){ + `cat $LTR.cln $LINE > $genome.LINE_LTR.raw.fa`; + $err = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -nolow -div 40 -lib $genome.LINE_LTR.raw.fa $SINE 2>&1`; + if ($err !~ /done/) { + `ln -s $SINE $SINE.masked` if $err =~ s/^.*(No repetitive sequences were detected.*)\s+$/Warning: No sequences were masked/s; + print STDERR "\n$err\n"; + } + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 80 -minscore 3000 -trf 0 -cleanN 1 -f $SINE.masked > $SINE.cln`; + } else { + `cp $SINE $SINE.cln`; + } + + +## clean LTRs and nonLTRs in TIRs and Helitrons +`cat $TIR.cln $HEL.cln | perl -nle 's/>/\\n>/g unless /^>/; print \$_' > $genome.TIR.Helitron.fa.stg1.raw`; +`cat $LTR.HQ $SINE.cln $LINE > $genome.LTR.SINE.LINE.fa`; +$err = `${repeatmasker}RepeatMasker -e ncbi -pa $threads -q -no_is -nolow -div 40 -lib $genome.LTR.SINE.LINE.fa $genome.TIR.Helitron.fa.stg1.raw 2>&1`; +if ($err !~ /done/) { + `ln -s $genome.TIR.Helitron.fa.stg1.raw $genome.TIR.Helitron.fa.stg1.raw.masked` if $err =~ s/^.*(No repetitive sequences were detected.*)\s+$/Warning: No sequences were masked/s; + print STDERR "\n$err\n"; + } +`perl $cleanup_tandem -misschar N -nc 50000 -nr 0.9 -minlen 80 -minscore 3000 -trf 0 -cleanN 1 -cleanT 1 -f $genome.TIR.Helitron.fa.stg1.raw.masked > $genome.TIR.Helitron.fa.stg1.raw.cln`; + + +## cluster TIRs and Helitrons and make stg1 raw library +`perl $cleanup_nested -in $genome.TIR.Helitron.fa.stg1.raw.cln -threads $threads -minlen 80 -cov 0.95 -blastplus $blast`; +`cat $LTR.cln $LINE $SINE.cln $genome.TIR.Helitron.fa.stg1.raw.cln.cln > $genome.EDTA.fa.stg1`; + +## generate clean intact TEs +`cat $LTRint.cln $LINE $SINE.cln $TIR.int.cln $HEL.int.cln > $genome.EDTA.intact.fa.cln`; + +## clean up the folder +`rm *.ndb *.not *.ntf *.nto *.cat.gz *.cat *.masked *.ori.out *.nhr *.nin *.nsq 2>/dev/null`; + +chdir '..'; diff --git a/conf/modules.config b/conf/modules.config index 9482021..82cff15 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -96,5 +96,15 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: 'EDTA:PROCESS_K' { + ext.prefix = { "${meta.id}.stg1" } + + publishDir = [ + path: { "${params.outdir}/stg1" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/modules/local/process_k/environment.yml b/modules/local/process_k/environment.yml new file mode 100644 index 0000000..e03f80c --- /dev/null +++ b/modules/local/process_k/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::blast=2.16.0 + - bioconda::repeatmasker=4.1.7 \ No newline at end of file diff --git a/modules/local/process_k/main.nf b/modules/local/process_k/main.nf new file mode 100644 index 0000000..7061d91 --- /dev/null +++ b/modules/local/process_k/main.nf @@ -0,0 +1,89 @@ +process PROCESS_K { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/91/91c1946f5edb90aa9d2c26eb14e7348f8f4e94dda03bdb2185b72cb3c2d54932/data': + 'community.wave.seqera.io/library/blast_repeatmasker:816962ca420d1d16' }" + + input: + tuple val(meta) , path(genome, name: 'genome') + path(ltr , name: "genome.EDTA.raw/genome.LTR.raw.fa") + path(ltrint , name: "genome.EDTA.raw/genome.LTR.intact.raw.fa") + path(sine , name: "genome.EDTA.raw/genome.SINE.raw.fa") + path(line , name: "genome.EDTA.raw/genome.LINE.raw.fa") + path(tir , name: "genome.EDTA.raw/genome.TIR.intact.raw.fa") + path(helitron , name: "genome.EDTA.raw/genome.Helitron.intact.raw.fa") + + output: + tuple val(meta), path('*.fasta') , emit: stg1_fa + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + def touch_ltr = ltr ? '' : "touch genome.EDTA.raw/genome.LTR.raw.fa" + def touch_ltrint = ltrint ? '' : "touch genome.EDTA.raw/genome.LTR.intact.raw.fa" + def touch_sine = sine ? '' : "touch genome.EDTA.raw/genome.SINE.raw.fa" + def touch_line = line ? '' : "touch genome.EDTA.raw/genome.LINE.raw.fa" + def touch_tir = tir ? '' : "touch genome.EDTA.raw/genome.TIR.intact.raw.fa" + def touch_helitron = helitron ? '' : "touch genome.EDTA.raw/genome.Helitron.intact.raw.fa" + """ + mkdir -p genome.EDTA.raw + $touch_ltr + $touch_ltrint + $touch_sine + $touch_line + $touch_tir + $touch_helitron + + PROGRAM_PATH=\$(dirname \$(which EDTA_processK.pl)) + + sed "s|\\\$script_path/bin|\$PROGRAM_PATH|g" \\ + \$PROGRAM_PATH/EDTA_processK.pl \\ + > EDTA_processK.pl + + perl \\ + EDTA_processK.pl \\ + -genome genome \\ + -ltr genome.EDTA.raw/genome.LTR.raw.fa \\ + -ltrint genome.EDTA.raw/genome.LTR.intact.raw.fa \\ + -sine genome.EDTA.raw/genome.SINE.raw.fa \\ + -line genome.EDTA.raw/genome.LINE.raw.fa \\ + -tir genome.EDTA.raw/genome.TIR.intact.raw.fa \\ + -helitron genome.EDTA.raw/genome.Helitron.intact.raw.fa \\ + $args \\ + ${task.cpus} + + mv \\ + genome.EDTA.combine/genome.EDTA.fa.stg1 \\ + ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + blast: \$(blastn -version | sed -n 's|Package: blast \\(.*\\)|\\1|p') + repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + blast: \$(blastn -version | sed -n 's|Package: blast \\(.*\\)|\\1|p') + repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/repeatmodeler_postprocess/main.nf b/modules/local/repeatmodeler_postprocess/main.nf index f538422..c1f6459 100644 --- a/modules/local/repeatmodeler_postprocess/main.nf +++ b/modules/local/repeatmodeler_postprocess/main.nf @@ -13,7 +13,7 @@ process REPEATMODELER_POSTPROCESS { output: tuple val(meta), path('*.RM2.fa') , emit: rm2_fa - tuple val(meta), path('*.LINE.raw.fa') , emit: line_raw + tuple val(meta), path('*.LINE.raw.fa') , emit: line_raw , optional: true path "versions.yml" , emit: versions when: @@ -37,9 +37,13 @@ process REPEATMODELER_POSTPROCESS { genome.RM2.fa \\ ${prefix}.RM2.fa - mv \\ - genome.LINE.raw.fa \\ - ${prefix}.LINE.raw.fa + if [[ -s genome.LINE.raw.fa ]]; then + mv \\ + genome.LINE.raw.fa \\ + ${prefix}.LINE.raw.fa + else + rm genome.LINE.raw.fa + fi cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -56,7 +60,6 @@ process REPEATMODELER_POSTPROCESS { if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.RM2.fa - touch ${prefix}.LINE.raw.fa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index d0cd760..e293c39 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -27,7 +27,8 @@ nextflow_pipeline { 'raw/line/*.pp.RM2.fa', 'raw/helitron/*.Helitron.intact.raw.fa', 'raw/helitron/*.Helitron.intact.raw.fa.anno.list', - 'raw/helitron/*.Helitron.intact.raw.gff3' + 'raw/helitron/*.Helitron.intact.raw.gff3', + 'stg1/*.stg1.fasta' ], null, ['**'] diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index e13891a..1ca54ba 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 21, + "successful tasks": 22, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -57,6 +57,11 @@ "TEsorter": "1.4.7", "mdust": "2006.10.17" }, + "PROCESS_K": { + "perl": "v5.32.1", + "blast": "2.16.0, build Nov 27 2024 09:40:57", + "repeatmasker": "4.1.7-p1" + }, "REPEATMODELER_BUILDDATABASE": { "repeatmodeler": "2.0.5" }, @@ -97,7 +102,6 @@ "raw/helitron/genome.pp.Helitron.intact.raw.fa.anno.list", "raw/helitron/genome.pp.Helitron.intact.raw.gff3", "raw/line", - "raw/line/genome.pp.LINE.raw.fa", "raw/line/genome.pp.RM2.fa", "raw/ltr", "raw/ltr/genome.pp.LTR.intact.raw.fa.anno.list", @@ -107,7 +111,9 @@ "raw/tir", "raw/tir/genome.pp.TIR.intact.raw.bed", "raw/tir/genome.pp.TIR.intact.raw.fa", - "raw/tir/genome.pp.TIR.intact.raw.gff3" + "raw/tir/genome.pp.TIR.intact.raw.gff3", + "stg1", + "stg1/genome.stg1.fasta" ] } ], @@ -115,6 +121,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-13T11:02:40.702113" + "timestamp": "2024-12-13T15:35:15.109085" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index 9d23a07..70d70de 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -21,6 +21,8 @@ include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/for include { FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT } from '../modules/local/format_helitronscanner_out/main' include { HELITRONSCANNER_POSTPROCESS } from '../modules/local/helitronscanner_postprocess/main' +include { PROCESS_K } from '../modules/local/process_k/main' + include { softwareVersionsToYAML } from '../modules/local/utils/main' include { idFromFileName } from '../modules/local/utils/main' @@ -249,6 +251,49 @@ workflow EDTA { ch_versions = ch_versions.mix(HELITRONSCANNER_POSTPROCESS.out.versions.first()) + // MODULE: PROCESS_K + ch_process_k_inputs = ch_sanitized_fasta + | join ( LTR_RETRIEVER_POSTPROCESS.out.raw_fa ) + | join ( LTR_RETRIEVER_POSTPROCESS.out.intact_raw_fa ) + | join ( ANNOSINE_POSTPROCESS.out.sine_fa , remainder: true ) + | join ( REPEATMODELER_POSTPROCESS.out.line_raw , remainder: true ) + | join ( TIR_LEARNER_POSTPROCESS.out.intact_raw_fa ) + | join ( HELITRONSCANNER_POSTPROCESS.out.raw_fa ) + | multiMap { meta, genome, ltr, ltrint, sine, line, tir, helitron -> + genome : [ meta, genome ] + ltr : ltr ?: [] + ltrint : ltrint ?: [] + sine : sine ?: [] + line : line ?: [] + tir : tir ?: [] + helitron: helitron ?: [] + } + + PROCESS_K ( + ch_process_k_inputs.genome, + ch_process_k_inputs.ltr, + ch_process_k_inputs.ltrint, + ch_process_k_inputs.sine, + ch_process_k_inputs.line, + ch_process_k_inputs.tir, + ch_process_k_inputs.helitron, + ) + + ch_versions = ch_versions.mix(PROCESS_K.out.versions.first()) + + // Warn: End of the pipeline if no inputs are available for ProcessK + ch_sanitized_fasta + | join ( LTR_RETRIEVER_POSTPROCESS.out.raw_fa , remainder: true ) + | join ( LTR_RETRIEVER_POSTPROCESS.out.intact_raw_fa , remainder: true ) + | join ( TIR_LEARNER_POSTPROCESS.out.intact_raw_fa , remainder: true ) + | join ( HELITRONSCANNER_POSTPROCESS.out.raw_fa , remainder: true ) + | map { meta, _genome, ltr, ltrint, tir, helitron -> + if ( !ltr || !ltrint || !tir || !helitron ) { + log.warn "One or more TE classes needed to complete EDTA were not found in genome '$meta.id'" + + ". Multiple processing steps are being skipped." + } + } + // Function: Save versions ch_versions = ch_versions | unique From b71316f50a4e27e1c3d806c6e650c8cd342f9f6b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 16 Dec 2024 16:04:57 +1300 Subject: [PATCH 40/49] Fixed conda version --- modules/local/process_k/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/process_k/environment.yml b/modules/local/process_k/environment.yml index e03f80c..ee63cb5 100644 --- a/modules/local/process_k/environment.yml +++ b/modules/local/process_k/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::blast=2.16.0 + - bioconda::blast=2.14.1 - bioconda::repeatmasker=4.1.7 \ No newline at end of file From 96daead66c3fd2772c59a0994f2d70c84e75f4be Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 16 Dec 2024 16:21:53 +1300 Subject: [PATCH 41/49] One more attempt to match conda vers --- modules/local/process_k/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/process_k/environment.yml b/modules/local/process_k/environment.yml index ee63cb5..9aec455 100644 --- a/modules/local/process_k/environment.yml +++ b/modules/local/process_k/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::blast=2.14.1 - - bioconda::repeatmasker=4.1.7 \ No newline at end of file + - bioconda::blast=2.16.0-hc155240_3 + - bioconda::repeatmasker=4.1.7p1-pl5321hdfd78af_1 \ No newline at end of file From 6b9f76d290aef9e0a186a9a696e4a3ac6964406b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 16 Dec 2024 16:37:46 +1300 Subject: [PATCH 42/49] Fixed syntax --- modules/local/process_k/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/process_k/environment.yml b/modules/local/process_k/environment.yml index 9aec455..8cab40b 100644 --- a/modules/local/process_k/environment.yml +++ b/modules/local/process_k/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::blast=2.16.0-hc155240_3 - - bioconda::repeatmasker=4.1.7p1-pl5321hdfd78af_1 \ No newline at end of file + - bioconda::blast=2.16.0=hc155240_3 + - bioconda::repeatmasker=4.1.7p1=pl5321hdfd78af_1 \ No newline at end of file From a9d9738853af1daa58c835adba6cf960b72c06f0 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 16 Dec 2024 16:49:02 +1300 Subject: [PATCH 43/49] Removed blast from versions --- modules/local/process_k/environment.yml | 4 ++-- modules/local/process_k/main.nf | 2 -- tests/nf-test/small/main.nf.test.snap | 1 - 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/modules/local/process_k/environment.yml b/modules/local/process_k/environment.yml index 8cab40b..e03f80c 100644 --- a/modules/local/process_k/environment.yml +++ b/modules/local/process_k/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::blast=2.16.0=hc155240_3 - - bioconda::repeatmasker=4.1.7p1=pl5321hdfd78af_1 \ No newline at end of file + - bioconda::blast=2.16.0 + - bioconda::repeatmasker=4.1.7 \ No newline at end of file diff --git a/modules/local/process_k/main.nf b/modules/local/process_k/main.nf index 7061d91..e385899 100644 --- a/modules/local/process_k/main.nf +++ b/modules/local/process_k/main.nf @@ -68,7 +68,6 @@ process PROCESS_K { cat <<-END_VERSIONS > versions.yml "${task.process}": perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') - blast: \$(blastn -version | sed -n 's|Package: blast \\(.*\\)|\\1|p') repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') END_VERSIONS """ @@ -82,7 +81,6 @@ process PROCESS_K { cat <<-END_VERSIONS > versions.yml "${task.process}": perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') - blast: \$(blastn -version | sed -n 's|Package: blast \\(.*\\)|\\1|p') repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') END_VERSIONS """ diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index 1ca54ba..8bd6b84 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -59,7 +59,6 @@ }, "PROCESS_K": { "perl": "v5.32.1", - "blast": "2.16.0, build Nov 27 2024 09:40:57", "repeatmasker": "4.1.7-p1" }, "REPEATMODELER_BUILDDATABASE": { From 09c711814725c47df4940227aef4e6dfd231c547 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 17 Dec 2024 14:10:59 +1300 Subject: [PATCH 44/49] Added final_filter --- .github/check_binaries.sh | 9 + bin/EDTA.pl | 861 ++++++++++++++++++ bin/setup_RepeatModeler_postprocess.sh | 2 +- bin/setup_combine_intact_TEs.sh | 14 + bin/setup_final_filter.sh | 31 + conf/modules.config | 27 +- modules/local/annosine_postprocess/main.nf | 8 +- .../local/combine_intact_tes/environment.yml | 10 + modules/local/combine_intact_tes/main.nf | 64 ++ modules/local/final_filter/environment.yml | 8 + modules/local/final_filter/main.nf | 69 ++ .../local/helitronscanner_postprocess/main.nf | 26 +- .../local/ltr_retriever_postprocess/main.nf | 26 +- modules/local/process_k/main.nf | 14 +- .../local/repeatmodeler_postprocess/main.nf | 14 +- modules/local/tir_learner_postprocess/main.nf | 20 +- tests/nf-test/small/main.nf.test | 22 +- tests/nf-test/small/main.nf.test.snap | 53 +- workflows/edta.nf | 52 ++ 19 files changed, 1236 insertions(+), 94 deletions(-) create mode 100755 bin/EDTA.pl create mode 100755 bin/setup_combine_intact_TEs.sh create mode 100755 bin/setup_final_filter.sh create mode 100644 modules/local/combine_intact_tes/environment.yml create mode 100644 modules/local/combine_intact_tes/main.nf create mode 100644 modules/local/final_filter/environment.yml create mode 100644 modules/local/final_filter/main.nf diff --git a/.github/check_binaries.sh b/.github/check_binaries.sh index 354d472..2fe4f9d 100755 --- a/.github/check_binaries.sh +++ b/.github/check_binaries.sh @@ -19,3 +19,12 @@ if [[ $EDTA_processK_pl_version != $bin_EDTA_processK_pl_version ]]; then echo 'Please synchronize bin/EDTA_processK.pl with EDTA_processK.pl' exit 1 fi + +EDTA_pl_version=$(md5sum EDTA.pl | cut -f1 -d' ') +bin_EDTA_pl_version=$(md5sum bin/EDTA.pl | cut -f1 -d' ') + +if [[ $EDTA_pl_version != $bin_EDTA_pl_version ]]; then + echo 'EDTA.pl != bin/EDTA.pl' + echo 'Please synchronize bin/EDTA.pl with EDTA.pl' + exit 1 +fi diff --git a/bin/EDTA.pl b/bin/EDTA.pl new file mode 100755 index 0000000..4e7f475 --- /dev/null +++ b/bin/EDTA.pl @@ -0,0 +1,861 @@ +#!/usr/bin/env perl +use warnings; +use strict; +use FindBin; +use File::Basename; +use Getopt::Long; +use Pod::Usage; +use POSIX qw(strftime); +use Cwd qw(abs_path); + +my $version = "v2.2.2"; +#v1.0 05/31/2019 +#v1.1 06/05/2019 +#v1.2 06/16/2019 +#v1.3 07/20/2019 +#v1.4 08/07/2019 +#v1.5 08/14/2019 +#v1.6 11/09/2019 +#v1.7 12/25/2019 +#v1.8 02/09/2020 +#v1.9 07/24/2020 +#v2.0 11/25/2021 +#v2.1 10/10/2022 +#v2.2 01/05/2024 +#v2.2.2 08/08/2024 + +print " +######################################################### +##### Extensive de-novo TE Annotator (EDTA) $version ##### +##### Shujun Ou (shujun.ou.1\@gmail.com) ##### +######################################################### +\n\nParameters: @ARGV\n\n\n"; + + +## Input: $genome +## Output: $genome.EDTA.TElib.fa + +my $usage = "\nThis is the Extensive de-novo TE Annotator that generates a high-quality +structure-based TE library. Usage: + +perl EDTA.pl [options] + --genome [File] The genome FASTA file. Required. + --species [Rice|Maize|others] Specify the species for identification of TIR + candidates. Default: others + --step [all|filter|final|anno] Specify which steps you want to run EDTA. + all: run the entire pipeline (default) + filter: start from raw TEs to the end. + final: start from filtered TEs to finalizing the run. + anno: perform whole-genome annotation/analysis after + TE library construction. + --overwrite [0|1] If previous raw TE results are found, decide to overwrite + (1, rerun) or not (0, default). + --cds [File] Provide a FASTA file containing the coding sequence (no introns, + UTRs, nor TEs) of this genome or its close relative. + --curatedlib [File] Provided a curated library to keep consistant naming and + classification for known TEs. TEs in this file will be + trusted 100%, so please ONLY provide MANUALLY CURATED ones. + This option is not mandatory. It's totally OK if no file is + provided (default). + --rmlib [File] Provide the RepeatModeler library containing classified TEs to enhance + the sensitivity especially for LINEs. If no file is provided (default), + EDTA will generate such file for you. + --sensitive [0|1] Use RepeatModeler to identify remaining TEs (1) or not (0, + default). This step may help to recover some TEs. + --anno [0|1] Perform (1) or not perform (0, default) whole-genome TE annotation + after TE library construction. + --rmout [File] Provide your own homology-based TE annotation instead of using the + EDTA library for masking. File is in RepeatMasker .out format. This + file will be merged with the structural-based TE annotation. (--anno 1 + required). Default: use the EDTA library for annotation. + --maxdiv [0-100] Maximum divergence (0-100%, default: 40) of repeat fragments comparing to + library sequences. + --evaluate [0|1] Evaluate (1) classification consistency of the TE annotation. + (--anno 1 required). Default: 1. + --exclude [File] Exclude regions (bed format) from TE masking in the MAKER.masked + output. Default: undef. (--anno 1 required). + --force [0|1] When no confident TE candidates are found: 0, interrupt and exit + (default); 1, use rice TEs to continue. + --u [float] Neutral mutation rate to calculate the age of intact LTR elements. + Intact LTR age is found in this file: *EDTA_raw/LTR/*.pass.list. + Default: 1.3e-8 (per bp per year, from rice). + --repeatmodeler [path] The directory containing RepeatModeler (default: read from ENV) + --repeatmasker [path] The directory containing RepeatMasker (default: read from ENV) + --annosine [path] The directory containing AnnoSINE_v2 (default: read from ENV) + --ltrretriever [path] The directory containing LTR_retriever (default: read from ENV) + --check_dependencies Check if dependencies are fullfiled and quit + --threads|-t [int] Number of theads to run this script (default: 4) + --debug [0|1] Retain intermediate files (default: 0) + --help|-h Display this help info +\n"; + +# pre-defined +my $genome = ''; +my $check_dependencies = undef; +my $species = "others"; +my $step = "ALL"; +my $overwrite = 0; #0, no rerun. 1, rerun even old results exist. +my $HQlib = ''; #curated library +my $RMlib = 'null'; #RepeatModeler library, classified +my $cds = ''; #a fasta file containing cds of this genome. +my $sensitive = 0; #0, will not run RepeatModeler to get remaining TEs (default). 1, run RepeatModeler +my $anno = 0; #0, will not annotate whole-genome TE (default). 1, annotate with RepeatMasker +my $rmout = ''; #a RM .out file for custom homology-based annotation. +my $evaluate = 1; #1 will evaluate the consistancy of the TE annotation +my $exclude = ''; #a bed file exclude from TE annotation +my $force = 0; #if there is no confident TE found in EDTA_raw, 1 will use rice TEs as raw lib, 0 will error and interrupt. +my $miu = 1.3e-8; #mutation rate, per bp per year, from rice +my $threads = 4; +my $maxdiv = 40; # maximum divergence from lib sequences for fragmented repeats +my $script_path = $FindBin::Bin; +my $EDTA_raw = "$script_path/EDTA_raw.pl"; +my $EDTA_process = "$script_path/EDTA_processK.pl"; +my $cleanup_proteins = "$script_path/bin/cleanup_proteins.pl"; +my $cleanup_TE = "$script_path/bin/cleanup_TE.pl"; +my $cleanup_tandem = "$script_path/bin/cleanup_tandem.pl"; +my $cleanup_nested = "$script_path/bin/cleanup_nested.pl"; +my $count_nested = "$script_path/bin/count_nested.pl"; +my $count_base = "$script_path/bin/count_base.pl"; +my $make_masked = "$script_path/bin/make_masked.pl"; +my $make_gff3 = "$script_path/bin/make_gff3_with_RMout.pl"; +my $protlib = "$script_path/database/alluniRefprexp082813"; +my $rice_LTR = "$script_path/database/rice7.0.0.liban.LTR"; +my $rice_SINE = "$script_path/database/rice7.0.0.liban.SINE"; +my $rice_LINE = "$script_path/database/rice7.0.0.liban.LINE"; +my $rice_TIR = "$script_path/database/rice7.0.0.liban.TIR"; +my $rice_helitron = "$script_path/database/rice7.0.0.liban.Helitron"; +my $rename_TE = "$script_path/bin/rename_TE.pl"; +#my $rename_RM = "$script_path/bin/rename_RM_TE.pl"; +my $call_seq = "$script_path/bin/call_seq_by_list.pl"; +my $buildSummary = "$script_path/bin/buildSummary.pl"; #modified from RepeatMasker. Robert M. Hubley (rhubley@systemsbiology.org) +my $filter_gff = "$script_path/bin/filter_gff3.pl"; +my $combine_RMrows = "$script_path/bin/combine_RMrows.pl"; +my $RMout2bed = "$script_path/bin/RMout2bed.pl"; +my $gff2RMout = "$script_path/bin/gff2RMout.pl"; +my $bed2gff = "$script_path/bin/bed2gff.pl"; +my $gff2bed = "$script_path/bin/gff2bed.pl"; +my $get_frag = "$script_path/bin/get_frag.pl"; +my $keep_nest = "$script_path/bin/keep_nest.pl"; +my $combine_overlap = "$script_path/bin/combine_overlap.pl"; +my $split_overlap = "$script_path/bin/split_overlap.pl"; +my $reclassify = "$script_path/bin/classify_by_lib_RM.pl"; +my $rename_by_list = "$script_path/bin/rename_by_list.pl"; +my $output_by_list = "$script_path/bin/output_by_list.pl"; +my $format_TElib = "$script_path/bin/format_TElib.pl"; +my $format_gff3 = "$script_path/bin/format_gff3.pl"; +my $add_id = "$script_path/bin/add_id.pl"; +my $div_table = "$script_path/bin/div_table2.pl"; +my $div_plot = "$script_path/bin/div_plot2.R"; +my $density_table = "$script_path/bin/density_table.py"; +my $density_plot = "$script_path/bin/density_plot.R"; +my $LTR_retriever = ""; +my $genometools = ""; +my $repeatmodeler = ""; +my $repeatmasker = ""; +my $TEsorter = ""; +my $blastplus = ""; +my $mdust = ""; +my $trf = ""; +my $GRF = ""; +my $annosine = ""; + +my $beta2 = 0; #0, beta2 is not ready. 1, developer mode. +#my $reanno = 0; #0, use existing whole-genome RM results (beta); 1, de novo Repeatmasker using the EDTA library (default) +my $debug = 0; +my $help = undef; + +# read parameters +if ( !GetOptions( 'genome=s' => \$genome, + 'species=s' => \$species, + 'step=s' => \$step, + 'overwrite=i' => \$overwrite, + 'curatedlib=s' => \$HQlib, + 'rmlib=s' => \$RMlib, + 'cds=s' => \$cds, + 'protlib=s' => \$protlib, + 'sensitive=s' => \$sensitive, + 'anno=i' => \$anno, + 'rmout=s' => \$rmout, + 'maxdiv=i' => \$maxdiv, + 'evaluate=i' => \$evaluate, + 'exclude=s' => \$exclude, + 'force=i' => \$force, + 'u=s' => \$miu, + 'repeatmodeler=s' => \$repeatmodeler, + 'repeatmasker=s' => \$repeatmasker, + 'tesorter=s' => \$TEsorter, + 'blast=s' => \$blastplus, + 'annosine=s' => \$annosine, + 'ltrretriever=s' => \$LTR_retriever, + 'threads|t=i' => \$threads, + 'check_dependencies!' => \$check_dependencies, + 'debug=i' => \$debug, + 'help|h!' => \$help ) ) + +{ + pod2usage( { -message => 'Failed to parse command line', + -verbose => 1, + -exitval => 1 } ); + } + +if ($help) { + pod2usage( { -verbose => 0, + -exitval => 0, + -message => "$usage\n" } ); + } + +if ( (! -s $genome) and (! $check_dependencies) ){ + pod2usage( { + -message => "At least 1 parameter is required:\n1) Input fasta file: --genome\n". + "$usage\n\n", + -verbose => 0, + -exitval => 2 } ); + } + +# get $maxdiv +$maxdiv = $maxdiv*100 if $maxdiv < 1; +$maxdiv =~ s/%//g; + +# check bolean +if ($maxdiv < 0 or $maxdiv > 100){die "The expected value for the div parameter is 0 - 100!\n"} +if ($overwrite != 0 and $overwrite != 1){ die "The expected value for the overwrite parameter is 0 or 1!\n"} +if ($sensitive != 0 and $sensitive != 1){ die "The expected value for the sensitive parameter is 0 or 1!\n"} +if ($anno != 0 and $anno != 1){ die "The expected value for the anno parameter is 0 or 1!\n"} +if ($evaluate != 0 and $evaluate != 1){ die "The expected value for the evaluate parameter is 0 or 1!\n"} +if ($force != 0 and $force != 1){ die "The expected value for the force parameter is 0 or 1!\n"} +if ($miu !~ /[0-9\.e\-]+/){ die "The expected value for the u parameter is float value without units!\n"} +if ($debug != 0 and $debug != 1){ die "The expected value for the debug parameter is 0 or 1!\n"} +if ($threads !~ /^[0-9]+$/){ die "The expected value for the threads parameter is an integer!\n"} + + +# define RepeatMasker -pa parameter +#my $rm_threads = int($threads/4); +my $rm_threads = $threads; + +chomp (my $date = `date`); +print "$date\tDependency checking:\n"; + +# check files and dependencies +die "The script EDTA_raw.pl is not found in $EDTA_raw!\n" unless -s $EDTA_raw; +die "The script EDTA_processK13.pl is not found in $EDTA_process!\n" unless -s $EDTA_process; +die "The script cleanup_proteins.pl is not found in $cleanup_proteins!\n" unless -s $cleanup_proteins; +die "The script cleanup_TE.pl is not found in $cleanup_TE!\n" unless -s $cleanup_TE; +die "The script cleanup_tandem.pl is not found in $cleanup_tandem!\n" unless -s $cleanup_tandem; +die "The script cleanup_nested.pl is not found in $cleanup_nested!\n" unless -s $cleanup_nested; +die "The script count_nested.pl is not found in $count_nested!\n" unless -s $count_nested; +die "The script count_base.pl is not found in $count_base!\n" unless -s $count_base; +die "The script make_masked.pl is not found in $make_masked!\n" unless -s $make_masked; +die "The script make_gff3_with_RMout.pl is not found in $make_gff3!\n" unless -s $make_gff3; +die "The protein-coding sequence library is not found in $protlib!\n" unless -s $protlib; +die "The rice LTR sequence library is not found in $rice_LTR!\n" unless -s $rice_LTR; +die "The rice SINE sequence library is not found in $rice_SINE!\n" unless -s $rice_SINE; +die "The rice LINE sequence library is not found in $rice_LINE!\n" unless -s $rice_LINE; +die "The rice TIR sequence library is not found in $rice_TIR!\n" unless -s $rice_TIR; +die "The rice Helitron sequence library is not found in $rice_helitron!\n" unless -s $rice_helitron; +die "The script rename_TE.pl is not found in $rename_TE!\n" unless -s $rename_TE; +die "The script call_seq_by_list.pl is not found in $call_seq!\n" unless -s $call_seq; +die "The script buildSummary.pl is not found in $buildSummary!\n" unless -s $buildSummary; +die "The script filter_gff3.pl is not found in $filter_gff!\n" unless -s $filter_gff; +die "The script RMout2bed.pl is not found in $RMout2bed!\n" unless -s $RMout2bed; +die "The script gff2RMout.pl is not found in $gff2RMout!\n" unless -s $gff2RMout; +die "The script combine_RMrows.pl is not found in $combine_RMrows!\n" unless -s $combine_RMrows; +die "The script bed2gff.pl is not found in $bed2gff!\n" unless -s $bed2gff; +die "The script gff2bed.pl is not found in $gff2bed!\n" unless -s $gff2bed; +die "The script get_frag.pl is not found in $get_frag!\n" unless -s $get_frag; +die "The script keep_nest.pl is not found in $keep_nest!\n" unless -s $keep_nest; +die "The script combine_overlap.pl is not found in $combine_overlap!\n" unless -s $combine_overlap; +die "The script split_overlap.pl is not found in $split_overlap!\n" unless -s $split_overlap; +die "The script classify_by_lib_RM.pl is not found in $reclassify!\n" unless -s $reclassify; +die "The script rename_by_list.pl is not found in $rename_by_list!\n" unless -s $rename_by_list; +die "The script output_by_list.pl is not found in $output_by_list!\n" unless -s $output_by_list; +die "The script format_gff3.pl is not found in $format_gff3!\n" unless -s $format_gff3; +die "The script add_id.pl is not found in $add_id!\n" unless -s $add_id; +die "The script div_table2.pl is not found in $div_table!\n" unless -s $div_table; +die "The script div_plot2.R is not found in $div_plot!\n" unless -s $div_plot; +die "The script density_table.py is not found in $density_table!\n" unless -s $density_table; +die "The script density_plot.R is not found in $density_plot!\n" unless -s $density_plot; + +# GenomeTools +chomp ($genometools=`command -v gt 2>/dev/null`) if $genometools eq ''; +$genometools =~ s/\s+$//; +$genometools = dirname($genometools) unless -d $genometools; +$genometools="$genometools/" if $genometools ne '' and $genometools !~ /\/$/; +die "Error: gt is not found in the genometools path $genometools!\n" unless -X "${genometools}gt"; +# AnnoSINE +chomp ($annosine=`command -v AnnoSINE_v2 2>/dev/null`) if $annosine eq ''; +$annosine =~ s/\s+$//; +$annosine = dirname($annosine) unless -d $annosine; +$annosine="$annosine/" if $annosine ne '' and $annosine !~ /\/$/; +die "Error: AnnoSINE is not found in the AnnoSINE path $annosine!\n" unless (-X "${annosine}AnnoSINE_v2"); +# LTR_retriever +chomp ($LTR_retriever=`command -v LTR_retriever 2>/dev/null`) if $LTR_retriever eq ''; +$LTR_retriever =~ s/\s+$//; +$LTR_retriever = dirname($LTR_retriever) unless -d $LTR_retriever; +$LTR_retriever="$LTR_retriever/" if $LTR_retriever ne '' and $LTR_retriever !~ /\/$/; +die "Error: LTR_retriever is not found in the LTR_retriever path $LTR_retriever!\n" unless -X "${LTR_retriever}LTR_retriever"; +# RepeatMasker +my $rand=int(rand(1000000)); +chomp ($repeatmasker=`command -v RepeatMasker 2>/dev/null`) if $repeatmasker eq ''; +$repeatmasker =~ s/\s+$//; +$repeatmasker = dirname($repeatmasker) unless -d $repeatmasker; +$repeatmasker="$repeatmasker/" if $repeatmasker ne '' and $repeatmasker !~ /\/$/; +die "Error: RepeatMasker is not found in the RepeatMasker path $repeatmasker!\n" unless -X "${repeatmasker}RepeatMasker"; +`cp $script_path/database/dummy060817.fa ./dummy060817.fa.$rand`; +my $RM_test=`${repeatmasker}RepeatMasker -e ncbi -q -pa 1 -no_is -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand 2>/dev/null`; +die "Error: The RMblast engine is not installed in RepeatMasker!\n" unless $RM_test=~s/done//gi; +`rm dummy060817.fa.$rand* 2>/dev/null`; +# RepeatModeler +chomp ($repeatmodeler=`command -v RepeatModeler 2>/dev/null`) if $repeatmodeler eq ''; +$repeatmodeler =~ s/\s+$//; +$repeatmodeler = dirname($repeatmodeler) unless -d $repeatmodeler; +$repeatmodeler="$repeatmodeler/" if $repeatmodeler ne '' and $repeatmodeler !~ /\/$/; +die "Error: RepeatModeler is not found in the RepeatModeler path $repeatmodeler!\n" unless -X "${repeatmodeler}RepeatModeler"; +# makeblastdb, blastn, blastx +chomp ($blastplus=`command -v makeblastdb 2>/dev/null`) if $blastplus eq ''; +$blastplus =~ s/\s+$//; +$blastplus = dirname($blastplus) unless -d $blastplus; +$blastplus="$blastplus/" if $blastplus ne '' and $blastplus !~ /\/$/; +die "Error: makeblastdb is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}makeblastdb"; +die "Error: blastn is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}blastn"; +die "Error: blastx is not found in the BLAST+ path $blastplus!\n" unless -X "${blastplus}blastx"; +# TEsorter +chomp ($TEsorter=`command -v TEsorter 2>/dev/null`) if $TEsorter eq ''; +$TEsorter =~ s/\s+$//; +$TEsorter = dirname($TEsorter) unless -d $TEsorter; +$TEsorter="$TEsorter/" if $TEsorter ne '' and $TEsorter !~ /\/$/; +die "Error: TEsorter is not found in the TEsorter path $TEsorter!\n" unless -X "${TEsorter}TEsorter"; +# mdust +chomp ($mdust=`command -v mdust 2>/dev/null`) if $mdust eq ''; +$mdust =~ s/\s+$//; +$mdust = dirname($mdust) unless -d $mdust; +$mdust = "$mdust/" if $mdust ne '' and $mdust !~ /\/$/; +die "Error: mdust is not found in the mdust path $mdust!\n" unless -X "${mdust}mdust"; +# trf +chomp ($trf=`command -v trf 2>/dev/null`) if $trf eq ''; +$trf=~s/\n$//; +`$trf 2>/dev/null`; +die "Error: Tandem Repeat Finder is not found in the TRF path $trf!\n" if $?==32256; +# GRF +chomp ($GRF = `command -v grf-main 2>/dev/null`) if $GRF eq ''; +$GRF =~ s/\n$//; +`$GRF 2>/dev/null`; +die "Error: The Generic Repeat Finder (GRF) is not found in the GRF path: $GRF\n" if $?==32256; + +print "\tAll passed!\n\n"; +exit if $check_dependencies; + +# make a softlink to the user-provided files +my $genome_file = basename($genome); +`ln -s $genome $genome_file` unless -e $genome_file; +$genome = $genome_file; + +# check if duplicated sequences found +my $id_mode = 0; #record the mode of id conversion. +my $id_len = `grep \\> $genome|perl -ne 'chomp; s/>//g; my \$len=length \$_; \$max=\$len if \$max<\$len; print "\$max\\n"'`; #find out the longest sequence ID length in the genome +$id_len =~ s/\s+$//; +$id_len = (split /\s+/, $id_len)[-1]; +my $raw_id = `grep \\> $genome|wc -l`; +my $old_id = `grep \\> $genome|sort -u|wc -l`; +if ($raw_id > $old_id){ + chomp ($date = `date`); + die "$date\tERROR: Identical sequence IDs found in the provided genome! Please resolve this issue and try again.\n"; + } + +# remove sequence annotations (content after the first space in sequence names) and replace special characters with _, convert non-ATGC bases into Ns +`perl -nle 'my \$info=(split)[0]; \$info=~s/[\\~!@#\\\$%\\^&\\*\\(\\)\\+\\\-\\=\\?\\[\\]\\{\\}\\:;",\\<\\/\\\\\|]+/_/g; \$info=~s/_+/_/g; \$info=~s/[^ATGCN]/N/gi unless /^>/; print \$info' $genome > $genome.$rand.mod`; + +# try to shortern sequences +my $id_len_max = 13; # allowed longest length of a sequence ID in the input file +if ($id_len > $id_len_max){ + chomp ($date = `date`); + print "$date\tThe longest sequence ID in the genome contains $id_len characters, which is longer than the limit ($id_len_max)\n"; + print "\tTrying to reformat seq IDs...\n\t\tAttempt 1...\n"; + `perl -lne 'chomp; if (s/^>+//) {s/^\\s+//; \$_=(split)[0]; s/(.{1,$id_len_max}).*/>\$1/g;} print "\$_"' $genome.$rand.mod > $genome.$rand.temp`; + my $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + chomp ($date = `date`); + if ($old_id == $new_id){ + $id_mode = 1; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + print "\t\tAttempt 2...\n"; + `perl -ne 'chomp; if (/^>/) {\$_=">\$1" if /([0-9]+)/;} print "\$_\n"' $genome.$rand.mod > $genome.$rand.temp`; + $new_id = `grep \\> $genome.$rand.temp|sort -u|wc -l`; + if ($old_id == $new_id){ + $id_mode = 2; + `mv $genome.$rand.temp $genome.mod`; + `rm $genome.$rand.mod 2>/dev/null`; + print "$date\tSeq ID conversion successful!\n\n"; + } else { + `rm $genome.$rand.temp $genome.$rand.mod 2>/dev/null`; + die "$date\tERROR: Fail to convert seq IDs to <= $id_len_max characters! Please provide a genome with shorter seq IDs.\n\n"; + } + } + } else { + `mv $genome.$rand.mod $genome.mod`; + } +$genome = "$genome.mod"; + +# check $HQlib +if ($HQlib ne ''){ + if (-s $HQlib){ + print "\tA custom library $HQlib is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.\n\n"; + chomp ($HQlib = `realpath $HQlib`); + my $HQlib_file = basename($HQlib); + `ln -s $HQlib $HQlib_file` unless -e $HQlib_file; + $HQlib = $HQlib_file; + } else { + die "\tERROR: The custom library $HQlib you specified is not found!\n\n"; + } + } + +# check $RMlib +if ($RMlib ne 'null'){ + if (-s $RMlib){ + print "\tA RepeatModeler library $RMlib is provided via --rmlib. Please make sure this is a RepeatModeler2 generated and classified library (some levels of unknown classification is OK).\n\n"; + chomp ($RMlib = `realpath $RMlib`); + `ln -s $RMlib $genome.RM2.raw.fa` unless -e "$genome.RM2.raw.fa"; + #`cp $RMlib $genome.RM2.raw.fa` unless -s "$genome.RM2.raw.fa"; + $RMlib = "$genome.RM2.raw.fa"; + } else { + die "\tERROR: The RepeatModeler library $RMlib you specified is not found!\n\n"; + } + }# else { + # `touch $genome.RM2.raw.fa 2>/dev/null`; + #} + +if ($cds ne ''){ + if (-s $cds){ + print "\tA CDS file $cds is provided via --cds. Please make sure this is the DNA sequence of coding regions only.\n\n"; + chomp ($cds = `realpath $cds`); + my $cds_file = basename($cds); + `ln -s $cds $cds_file` unless -e $cds_file; + $cds = $cds_file; + } else { + die "\tERROR: The CDS file $cds you specified is not found!\n\n"; + } + } + +if ($rmout ne ''){ + if (-s $rmout){ + print "\tA RepeatMasker .out file $rmout is provided via --rmout.\n\n"; + chomp ($rmout = `realpath $rmout`); + } else { + die "\tERROR: The RepeatMasker .out file $rmout you specified is not found!\n\n"; + } + } + +if ($exclude ne ''){ + if (-s $exclude){ + print "\tA BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.\n\n"; + my $exclude_file = basename($exclude); + `ln -s $exclude $exclude_file ` unless -e $exclude_file; + $exclude = $exclude_file; + } else { + die "\tERROR: The exclusion BED file $exclude you specified is not found!\n\n"; + } + } + +$step = uc $step; +goto $step; + + +############################################################ +####### Get raw LTR/SINE/LINE/TIR/Helitron candidates ###### +############################################################ + +ALL: + +# report status +chomp ($date = `date`); +print "$date\tObtain raw TE libraries using various structure-based programs: \n"; + +# Get raw TE candidates +`perl $EDTA_raw --genome $genome --overwrite $overwrite --species $species --u $miu --threads $threads --genometools $genometools --ltrretriever $LTR_retriever --blastplus $blastplus --tesorter $TEsorter --GRF $GRF --trf_path $trf --repeatmasker $repeatmasker --repeatmodeler $repeatmodeler --annosine $annosine --convert_seq_name 0 --rmlib $RMlib`; + +chdir "$genome.EDTA.raw"; + +# Force to use rice TEs when raw.fa is empty +if ($force eq 1){ + `cp $rice_LTR $genome.LTR.raw.fa` unless -s "$genome.LTR.raw.fa"; + `cp $rice_LTR $genome.LTR.intact.raw.fa` unless -s "$genome.LTR.intact.raw.fa"; + `cp $rice_LINE $genome.LINE.raw.fa` unless -s "$genome.LINE.raw.fa"; + `cp $rice_SINE $genome.SINE.raw.fa` unless -s "$genome.SINE.raw.fa"; + `cp $rice_TIR $genome.TIR.intact.raw.fa` unless -s "$genome.TIR.intact.raw.fa"; + `cp $rice_helitron $genome.Helitron.intact.raw.fa` unless -s "$genome.Helitron.intact.raw.fa"; + } + +# check results and report status +die "ERROR: Raw LTR results not found in $genome.EDTA.raw/$genome.LTR.raw.fa and $genome.EDTA.raw/$genome.LTR.intact.raw.fa\n\tIf you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the --force 1 parameter to overwrite this check\n" unless (-s "$genome.LTR.raw.fa" and -s "$genome.LTR.intact.raw.fa"); +die "ERROR: Raw SINE results not found in $genome.EDTA.raw/$genome.SINE.raw.fa\n\tIf you believe the program is working properly, this may be caused by the lack of SINEs in your genome.\n" unless -e "$genome.SINE.raw.fa"; # allow empty file +die "ERROR: Raw LINE results not found in $genome.EDTA.raw/$genome.LINE.raw.fa\n\tIf you believe the program is working properly, this may be caused by the lack of LINEs in your genome.\n" unless -e "$genome.LINE.raw.fa"; # allow empty file +die "ERROR: Raw TIR results not found in $genome.EDTA.raw/$genome.TIR.intact.raw.fa\n\tIf you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this check\n" unless -s "$genome.TIR.intact.raw.fa"; +die "ERROR: Raw Helitron results not found in $genome.EDTA.raw/$genome.Helitron.intact.raw.fa\n\tIf you believe the program is working properly, this may be caused by the lack of intact Helitrons in your genome. Consider to use the --force 1 parameter to overwrite this check\n" unless -s "$genome.Helitron.intact.raw.fa"; + +# combine intact TEs +`cat $genome.LTR.intact.raw.fa $genome.TIR.intact.raw.fa $genome.Helitron.intact.raw.fa > $genome.EDTA.intact.raw.fa`; +`cat $genome.TIR.intact.raw.bed $genome.Helitron.intact.raw.bed | perl $bed2gff - TE_struc > $genome.EDTA.intact.gff3.temp`; +`cat $genome.LTR.intact.raw.gff3 >> $genome.EDTA.intact.gff3.temp`; +`sort -sV -k1,1 -k4,4 $genome.EDTA.intact.gff3.temp | grep -v '^#' > $genome.EDTA.intact.raw.gff3; rm $genome.EDTA.intact.gff3.temp`; + +chomp ($date = `date`); +print "$date\tObtain raw TE libraries finished. +\tAll intact TEs found by EDTA: \n\t\t$genome.EDTA.intact.raw.fa \n\t\t$genome.EDTA.intact.raw.gff3\n\n"; +chdir ".."; + + +############################################################ +####### Filter LTR/SINE/LINE/TIR/Helitron candidates ####### +############################################################ + +FILTER: + +# report status +chomp ($date = `date`); +print "$date\tPerform EDTA advance filtering for raw TE candidates and generate the stage 1 library: \n\n"; + +# remove existing results +`rm ./$genome.EDTA.combine/* 2>/dev/null` if $overwrite == 1; + +# Filter raw TE candidates and the make stage 1 library +`perl $EDTA_process -genome $genome -ltr $genome.EDTA.raw/$genome.LTR.raw.fa -ltrint $genome.EDTA.raw/$genome.LTR.intact.raw.fa -line $genome.EDTA.raw/$genome.LINE.raw.fa -sine $genome.EDTA.raw/$genome.SINE.raw.fa -tir $genome.EDTA.raw/$genome.TIR.intact.raw.fa -helitron $genome.EDTA.raw/$genome.Helitron.intact.raw.fa -repeatmasker $repeatmasker -blast $blastplus -threads $threads`; + +# check results, remove intermediate files, and report status +die "ERROR: Stage 1 library not found in $genome.EDTA.combine/$genome.EDTA.fa.stg1" unless -s "$genome.EDTA.combine/$genome.EDTA.fa.stg1"; +chdir "$genome.EDTA.combine"; +`rm ./$genome.LTR.raw.fa*Q* ./$genome.LTR.intact.raw.fa*Q* ./$genome.TIR.intact.raw.fa*Q* ./$genome.Helitron.intact.raw.fa*Q* ./$genome.TIR.Helitron.fa*Q* $genome*tbl $genome*out $genome*cleanup $genome*RMoutput $genome*stg1.raw* $genome.LTR.raw.fa-* $genome.LTR.intact.raw.fa-* $genome.TIR.intact.raw.fa-* $genome.Helitron.intact.raw.fa-* $genome.LINE_LTR.raw.fa $genome.LTR.SINE.LINE.fa *.ndb *.not *.ntf *.nto *.cat.gz *.cat *.masked *.ori.out *.nhr *.nin *.nsq 2>/dev/null` unless $debug eq 1; + +chdir ".."; +chomp ($date = `date`); +print "$date\tEDTA advance filtering finished.\n\n"; + + +#################################### +###### Final purge CDS in TEs ###### +#################################### + +FINAL: + +# report status +chomp ($date = `date`); +print "$date\tPerform EDTA final steps to generate a non-redundant comprehensive TE library.\n\n"; + +# Make the final working directory +`mkdir $genome.EDTA.final` unless -e "$genome.EDTA.final" && -d "$genome.EDTA.final"; +chdir "$genome.EDTA.final"; +`rm ./* 2>/dev/null` if $overwrite == 1; +`cp ../$genome.EDTA.raw/$genome.RM2.fa ./`; +`cp ../$genome.EDTA.combine/$genome.EDTA.fa.stg1 ./`; +`cp ../$cds ./` if $cds ne ''; +`cp ../$HQlib ./` if $HQlib ne ''; +`cp ../$genome.EDTA.combine/$genome.EDTA.intact.fa.cln ./$genome.EDTA.intact.fa.cln`; +#`cp ../$genome.EDTA.raw/$genome.EDTA.intact.raw.fa ./`; +`cp ../$genome.EDTA.raw/$genome.EDTA.intact.raw.gff3 ./`; +`cp ../$exclude ./` if $exclude ne ''; + +# identify remaining TEs in the filtered RM2 library +if ($sensitive == 1 and -s "$genome.RM2.fa"){ + print "\tFilter RepeatModeler results that are ignored in the raw step.\n\n"; + chomp ($date = `date`); + my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div 40 -lib $genome.EDTA.fa.stg1 $genome.RM2.fa 2>/dev/null`; + `cp $genome.RM2.fa $genome.RM2.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i; + # clean up tandem and coding sequences in the RM2 library + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 1 -trf_path $trf -cleanN 1 -cleanT 1 -f $genome.RM2.fa.masked > $genome.RM2.fa.stg1`; + `perl $cleanup_proteins -seq $genome.RM2.fa.stg1 -rmdnate 0 -rmline 0 -rmprot 1 -protlib $protlib -blast $blastplus -threads $threads`; + if (-s "$genome.RM2.fa.stg1.clean"){ + `cat $genome.EDTA.fa.stg1 $genome.RM2.fa.stg1.clean > $genome.EDTA.raw.fa`; + } else { + print "\t\tNo extra repeat sequences found in the RepeatModeler output.\n\n"; + `cp $genome.EDTA.fa.stg1 $genome.EDTA.raw.fa`; + } + } else { + print "\tSkipping the RepeatModeler results (--sensitive 0).\n\t\tRun EDTA.pl --step final --sensitive 1 if you want to add RepeatModeler results.\n\n"; + `cp $genome.EDTA.fa.stg1 $genome.EDTA.raw.fa`; + } + +# remove CDS in the non-redundant library and intact TEs +if (-s "$cds"){ + # report status + chomp ($date = `date`); + + # cleanup TE-related sequences in the CDS file with TEsorter + print "$date\tClean up TE-related sequences in the CDS file with TEsorter.\n\n"; + `perl $cleanup_TE -cds $cds -minlen 300 -tesorter $TEsorter -repeatmasker $repeatmasker -t $threads -rawlib $genome.EDTA.raw.fa 2>/dev/null`; + `rm ./$cds ./$cds.code.r* 2>/dev/null` unless $debug eq 1; + die "\tERROR: The $cds file is empty after TE clean up. Please check the file and $cds.code.noTE.\n\n" unless -s "$cds.code.noTE"; + $cds = "$cds.code.noTE"; + + # remove cds-related sequences in the EDTA library + print "\tRemove CDS-related sequences in the EDTA library.\n\n"; + my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.raw.fa 2>/dev/null`; + `cp $genome.EDTA.raw.fa $genome.EDTA.raw.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i; + `perl $cleanup_tandem -misschar N -Nscreen 1 -nc 1000 -nr 0.3 -minlen 80 -maxlen 5000000 -trf 0 -cleanN 1 -cleanT 1 -f $genome.EDTA.raw.fa.masked > $genome.EDTA.raw.fa.cln`; + + # remove cds-related sequences in intact TEs + print "\tRemove CDS-related sequences in intact TEs.\n\n"; + $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div 40 -cutoff 225 -lib $cds $genome.EDTA.intact.fa.cln 2>/dev/null`; + `cp $genome.EDTA.intact.fa.cln $genome.EDTA.intact.fa.cln.masked` if $rm_status =~ /No repetitive sequences were detected/i; + `perl $cleanup_tandem -misschar N -Nscreen 1 -nc 1000 -nr 0.8 -minlen 80 -maxlen 5000000 -trf 0 -cleanN 0 -f $genome.EDTA.intact.fa.cln.masked > $genome.EDTA.intact.fa.cln.rmCDS`; + `perl $output_by_list 1 $genome.EDTA.intact.fa.cln 1 $genome.EDTA.intact.fa.cln.masked.cleanup -ex -FA > $genome.EDTA.intact.fa.cln2`; + } else { + print "\tSkipping the CDS cleaning step (--cds [File]) since no CDS file is provided or it's empty.\n\n"; + copy_file("$genome.EDTA.raw.fa", "./$genome.EDTA.raw.fa.cln"); + copy_file("$genome.EDTA.intact.fa.cln", "./$genome.EDTA.intact.fa.cln2"); + } + +# Final rounds of redundancy removal and make final EDTA library +`perl $cleanup_nested -in $genome.EDTA.raw.fa.cln -threads $threads -minlen 80 -cov 0.95 -blastplus $blastplus 2>/dev/null`; + +# rename all TEs in the EDTA library +`perl $rename_TE $genome.EDTA.raw.fa.cln.cln > $genome.EDTA.TElib.fa`; +#`perl $rename_TE $genome.EDTA.raw.fa.cln.cln | perl $format_TElib - > $genome.EDTA.TElib.fa`; + +# identify novel TEs using the user provided $HQlib +if ($HQlib ne ''){ + # report status + chomp ($date = `date`); + print "$date\tCombine the high-quality TE library $HQlib with the EDTA library:\n\n"; + + # remove known TEs in the EDTA library + my $rm_status = `${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div 40 -lib $HQlib $genome.EDTA.TElib.fa 2>/dev/null`; + `cp $genome.EDTA.TElib.fa $genome.EDTA.TElib.fa.masked` if $rm_status =~ /No repetitive sequences were detected/i; + `perl $cleanup_tandem -misschar N -nc 50000 -nr 0.8 -minlen 80 -minscore 3000 -trf 0 -cleanN 1 -cleanT 0 -f $genome.EDTA.TElib.fa.masked > $genome.EDTA.TElib.novel.fa`; + rename "$genome.EDTA.TElib.fa", "$genome.EDTA.TElib.ori.fa"; + `cat $HQlib $genome.EDTA.TElib.novel.fa > $genome.EDTA.TElib.fa`; + copy_file("$genome.EDTA.TElib.novel.fa", ".."); + } + +# reclassify intact TEs with the TE lib #113 +`${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div 40 -lib $genome.EDTA.TElib.fa $genome.EDTA.intact.fa.cln2 2>/dev/null` unless (-s "$genome.EDTA.intact.fa.cln2.out" and $overwrite == 0); +die "ERROR: The masked file for $genome.EDTA.intact.fa.cln2 is not found! The RepeatMasker annotation on this file may be failed. Please check the $genome.EDTA.TElib.fa file for sequence naming formats especially when you provide a library via --curatedlib.\n" unless -s "$genome.EDTA.intact.fa.cln2.out"; +`perl $reclassify -seq $genome.EDTA.intact.fa.cln2 -RM $genome.EDTA.intact.fa.cln2.out -cov 80 -len 80 -iden 60`; # 80-80-60 + +# remove inconsistently classified intact TEs and generate the final intact TEs +`perl $output_by_list 1 $genome.EDTA.intact.fa.cln2.rename 1 $genome.EDTA.intact.fa.cln2.false.list -ex -FA > $genome.EDTA.intact.fa`; + + +## generate clean intact gff3 +my $intact_gff_head = "##This file follows the ENSEMBL standard: https://useast.ensembl.org/info/website/upload/gff3.html +##Column 3: Sequence Ontology of repeat features. Please refer to the SO database for more details: http://www.sequenceontology.org/. In cases where the SO database does not have the repeat feature, tentative SO names are used, with a full list included in EDTA/bin/TE_Sequence_Ontology.txt (Enhancement notes), and the sequence_ontology in Column 9 uses the closest parent SO. +##Column 9: +## ID: unique ID for this feature in the genome. +## classification: Same as Column 3 but formatted following the RepeatMasker naming convention. +## sequence_ontology: Sequence Ontology ID of the feature. +## identity: Sequence identity (0-1) between terminal sequences for structurally annotated TIR elements. +## ltr_identity: Sequence identity (0-1) between the left and right LTR regions for structurally annotated LTR elements. +## Name: Repeat family name. Some may be shown as coordinates, which are single-copy and structrually identified elements that are not included in the repeat library. +## method=structural: Indicate this entry is produced by structural annotation. +## motif/TSD/TIR: structural features of structurally annotated LTR and TIR elements. +##For more details about this file, please refer to the EDTA wiki: https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A +##seqid source sequence_ontology start end score strand phase attributes"; + +# update the family names in the intact.raw.gff3 file +`perl $rename_by_list $genome.EDTA.intact.raw.gff3 $genome.EDTA.intact.fa.cln2.rename.list 1 > $genome.EDTA.intact.raw.gff3.rename`; +`sed 's/.*Name=//; s/;Classifica.*//' $genome.EDTA.intact.raw.gff3.rename | sort -u > $genome.EDTA.intact.raw.gff3.rename.famlist`; + +# get a dirty list of intact.gff +`grep \\> $genome.EDTA.intact.fa | sed 's/>//; s/#.*//' | perl $output_by_list 1 $genome.EDTA.intact.raw.gff3.rename.famlist 1 - -ex | awk '{print "Name\\t"\$1"\\nParent\\t"\$1"\\nID\\t"\$1}' > $genome.EDTA.intact.raw.gff3.rename.dirtlist`; + +# first attempt purging the gff3 +`perl $filter_gff $genome.EDTA.intact.raw.gff3.rename $genome.EDTA.intact.raw.gff3.rename.dirtlist > $genome.EDTA.intact.gff3`; + +# remake the remove list and purge again +`perl -nle 'my \$id = \$1 if /=(repeat_region[0-9]+);/; print "Parent\\t\$id\nName\\t\$id" if defined \$id' $genome.EDTA.intact.raw.gff3.rename.removed >> $genome.EDTA.intact.raw.gff3.rename.dirtlist`; +`echo "##gff-version 3\n##date $date\n##This file contains repeats annotated by EDTA $version based on structural features.\n$intact_gff_head" > $genome.EDTA.intact.gff3`; +`perl $filter_gff $genome.EDTA.intact.raw.gff3.rename $genome.EDTA.intact.raw.gff3.rename.dirtlist >> $genome.EDTA.intact.gff3`; + +# format gff3 +`perl $format_gff3 $genome.EDTA.intact.gff3 > gff3.temp.gff3; mv gff3.temp.gff3 $genome.EDTA.intact.gff3`; + +# add TE_IDs to the intact.fa sequence IDs +`perl $add_id -fa $genome.EDTA.intact.fa -gff $genome.EDTA.intact.gff3 > $genome.EDTA.intact.fa.renamed; mv $genome.EDTA.intact.fa.renamed $genome.EDTA.intact.fa`; + +# check results +die "ERROR: Final TE library not found in $genome.EDTA.TElib.fa" unless -s "$genome.EDTA.TElib.fa"; +die "ERROR: Intact TE annotation not found in $genome.EDTA.intact.gff3" unless -s "$genome.EDTA.intact.gff3"; +copy_file("$genome.EDTA.TElib.fa", ".."); +copy_file("$genome.EDTA.intact.fa", ".."); +copy_file("$genome.EDTA.intact.gff3", ".."); + +# remove intermediate files +`rm $genome.EDTA.intact.fa.cln.* $genome.EDTA.raw.fa.* $genome.EDTA.TElib.fa.* $genome.LTR.TIR.Helitron.fa.stg1.* $genome.masked *.cat.gz 2>/dev/null` if $debug eq 0; + +# report status +chomp ($date = `date`); +print "$date\tEDTA final stage finished! You may check out: + The final EDTA TE library: $genome.EDTA.TElib.fa\n"; +print " Family names of intact TEs have been updated by $HQlib: $genome.EDTA.intact.gff3\n" if $HQlib ne ''; +print " Comparing to the provided library, EDTA found these novel TEs: $genome.EDTA.TElib.novel.fa + The provided library has been incorporated into the final library: $genome.EDTA.TElib.fa\n\n" if $HQlib ne ''; +chdir ".."; + + +##################################### +###### Post-library annotation ###### +##################################### + +ANNO: +if ($anno == 1){ + # report status + chomp ($date = `date`); + print "$date\tPerform post-EDTA analysis for whole-genome annotation:\n\n"; + + # Make the post-library annotation working directory + `mkdir $genome.EDTA.anno` unless -e "$genome.EDTA.anno" && -d "$genome.EDTA.anno"; + chdir "$genome.EDTA.anno"; + `rm ./* 2>/dev/null` if $overwrite == 1; + `rm $genome.EDTA.TElib.fa* 2>/dev/null`; # clean up libraries + `cp ../$genome.EDTA.final/$genome.EDTA.TElib.fa ./`; + `cp ../$genome.EDTA.final/$genome.EDTA.intact.gff3 ./`; + `cp ../$exclude ./` if $exclude ne ''; + `ln -s ../$genome $genome` unless -e $genome; + + my $gff_head = "##This file follows the ENSEMBL standard: https://useast.ensembl.org/info/website/upload/gff3.html +##Column 3: Sequence Ontology of repeat features. Please refer to the SO database for more details: http://www.sequenceontology.org/. In cases where the SO database does not have the repeat feature, tentative SO names are used, with a full list included in EDTA/bin/TE_Sequence_Ontology.txt (Enhancement notes), and the sequence_ontology in Column 9 uses the closest parent SO. +##Column 7: The Smith-Waterman score generated by RepeatMasker, only available for homology entries. +##Column 9: +## ID: unique ID for this feature in the genome. +## classification: Same as Column 3 but formatted following the RepeatMasker naming convention. +## sequence_ontology: Sequence Ontology ID of the feature. +## identity: Sequence identity (0-1) between the library sequence and the target region. +## ltr_identity: Sequence identity (0-1) between the left and right LTR regions for structurally annotated LTR elements. +## Name: Repeat family name. Some may be shown as coordinates, which are single-copy and structrually identified elements that are not included in the repeat library. +## method: Indicate if this entry is produced by structural annotation or homology annotation. +## motif/TSD/TIR: structural features of structurally annotated LTR and TIR elements. +##For more details about this file, please refer to the EDTA wiki: https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A +##seqid source sequence_ontology start end score strand phase attributes"; + + # annotate TEs using RepeatMasker + if ($rmout ne ''){ + print STDERR "$date\tA RepeatMasker result file $rmout is provided! Will use this file without running RepeatMasker.\n\n"; + if (-e "$genome.out"){ + my $old_rmout = `ls -l $genome.out|perl -nle 'my (\$month, \$day, \$time) = (split)[6,7,8]; \$time =~ s/://; print "\${month}_\${day}_\$time"'`; + chomp $old_rmout; + print "\t$genome.out exists in the $genome.EDTA.anno folder, renamed file to ${genome}_$old_rmout.out\n\n"; + `mv $genome.out ${genome}_$old_rmout.out`; + } + `ln -s $rmout $genome.out`; + } else { + print STDERR "$date\tHomology-based annotation of TEs using $genome.EDTA.TElib.fa from scratch.\n\n"; + `${repeatmasker}RepeatMasker -e ncbi -pa $rm_threads -q -no_is -nolow -div $maxdiv -lib $genome.EDTA.TElib.fa $genome 2>/dev/null`; + } + die "ERROR: RepeatMasker results not found in $genome.out!\n\n" unless -s "$genome.out" or -s "$genome.mod.out"; + + # exclude regions from TE annotation and make whole-genome TE annotation + `perl $make_masked -genome $genome -rmout $genome.out -maxdiv $maxdiv -minscore 300 -minlen 80 -hardmask 1 -misschar N -threads $threads -exclude $exclude`; + # combine RepeatMasker lines that appears to be the same element + `perl $combine_RMrows -rmout $genome.out.new -maxdiv 3.5 -maxgap 35`; + `mv $genome.out.new.cmb $genome.EDTA.RM.out`; + `perl $RMout2bed $genome.EDTA.RM.out > $genome.EDTA.RM.bed`; # a regular enriched bed + `perl $bed2gff $genome.EDTA.RM.bed TE_homo > $genome.EDTA.RM.gff3`; + `perl $gff2bed $genome.EDTA.RM.gff3 homology > $genome.EDTA.RM.bed`; # add the last column to this bed + + # combine homology-based and strutrual-based annotation (partly overlapping) + `perl $gff2bed $genome.EDTA.intact.gff3 structural > $genome.EDTA.intact.bed`; + `perl $combine_overlap $genome.EDTA.intact.bed $genome.EDTA.intact.bed.cmb 5`; + `perl $get_frag $genome.EDTA.RM.bed $genome.EDTA.intact.bed.cmb $threads`; + `perl $keep_nest $genome.EDTA.intact.bed $genome.EDTA.RM.bed $threads`; + `grep homology $genome.EDTA.intact.bed-$genome.EDTA.RM.bed > $genome.EDTA.intact.bed-$genome.EDTA.RM.bed.homo`; + `sort -suV $genome.EDTA.intact.bed-$genome.EDTA.RM.bed.homo $genome.EDTA.RM.bed-$genome.EDTA.intact.bed.cmb > $genome.EDTA.homo.bed`; + `perl $bed2gff $genome.EDTA.homo.bed TE_homo > $genome.EDTA.homo.gff3`; + `cat $genome.EDTA.intact.gff3 $genome.EDTA.homo.gff3 > $genome.EDTA.TEanno.gff3.raw`; + `grep -v '^#' $genome.EDTA.TEanno.gff3.raw | sort -sV -k1,1 -k4,4 | perl -0777 -ne '\$date=\`date\`; \$date=~s/\\s+\$//; print "##gff-version 3\\n##date \$date\\n##This file contains repeats annotated by EDTA $version with both structural and homology methods. Repeats can be overlapping due to nested insertions.\\n$gff_head\\n\$_"' - > $genome.EDTA.TEanno.gff3`; + `perl $format_gff3 $genome.EDTA.TEanno.gff3 > gff3.temp.gff3; mv gff3.temp.gff3 $genome.EDTA.TEanno.gff3`; + `rm $genome.EDTA.TEanno.gff3.raw 2>/dev/null`; + + # make non-overlapping annotation + `perl $gff2bed $genome.EDTA.TEanno.gff3 structural > $genome.EDTA.TEanno.bed`; + `perl $split_overlap $genome.EDTA.TEanno.bed $genome.EDTA.TEanno.split.bed`; + `echo "##gff-version 3\n##date $date\n##This file contains all repeats annotated by EDTA $version in the split format (non-overlapping). Repeats can be broken into pieces by nested insertions.\n$gff_head" > $genome.EDTA.TEanno.split.gff3`; + `perl $bed2gff $genome.EDTA.TEanno.split.bed | grep -v '^#' >> $genome.EDTA.TEanno.split.gff3`; + `perl $format_gff3 $genome.EDTA.TEanno.split.gff3 > gff3.temp.gff3; mv gff3.temp.gff3 $genome.EDTA.TEanno.split.gff3`; + `perl $gff2RMout $genome.EDTA.TEanno.split.gff3 $genome.EDTA.TEanno.split.out`; + + # make plots + `perl $div_table $genome.EDTA.TEanno.bed $genome $genome`; + `Rscript $div_plot $genome.div_long $genome 2>/dev/null`; + `python $density_table -genome $genome -gff $genome.EDTA.TEanno.split.gff3 > $genome.EDTA.TEanno.split.density`; + `Rscript $density_plot $genome.EDTA.TEanno.split.density 2>/dev/null`; + `mv chromosome_density_plots.pdf $genome.EDTA.TEanno.density_plots.pdf`; + + # make summary table for the non-overlapping annotation + `perl $count_base $genome > $genome.stats`; + `perl -nle 'my (\$chr, \$s, \$e, \$anno, \$dir, \$supfam)=(split)[0,1,2,3,8,12]; print "10000 0.001 0.001 0.001 \$chr \$s \$e NA \$dir \$anno \$supfam"' $genome.EDTA.TEanno.split.bed > $genome.EDTA.TEanno.out`; + `perl $buildSummary -maxDiv 40 -stats $genome.stats $genome.EDTA.TEanno.out > $genome.EDTA.TEanno.sum 2>/dev/null`; + my $tot_TE = `grep Total $genome.EDTA.TEanno.sum|grep %|awk '{print \$4}'`; + chomp $tot_TE; + + # make low-threshold masked genome for MAKER + `perl $make_masked -genome $genome -rmout $genome.out -maxdiv 30 -minscore 1000 -minlen 1000 -hardmask 1 -misschar N -threads $threads -exclude $exclude` unless (-s "$genome.MAKER.masked" and $overwrite == 0); + `mv $genome.new.masked $genome.MAKER.masked`; + my $maker_TE = `perl $count_base $genome.MAKER.masked`; + $maker_TE = (split /\s+/, $maker_TE)[3]; + $maker_TE = sprintf("%.2f%%", $maker_TE*100); + + # check results and report status + die "ERROR: TE annotation results not found in $genome.EDTA.TEanno.gff3!\n\n" unless -s "$genome.EDTA.TEanno.gff3"; + print "ERROR: The masked genome for MAKER annotation is not found in $genome.MAKER.masked!\n\n" unless -s "$genome.MAKER.masked"; + chomp ($date = `date`); + print "$date\tTE annotation using the EDTA library has finished! Check out:\n"; + print "\t\tWhole-genome TE annotation (total TE: $tot_TE): $genome.EDTA.TEanno.gff3\n"; + print "\t\tWhole-genome TE annotation summary: $genome.EDTA.TEanno.sum\n"; + print "\t\tWhole-genome TE divergence plot: ${genome}_divergence_plot.pdf\n"; + print "\t\tWhole-genome TE density plot: $genome.EDTA.TEanno.density_plots.pdf\n"; + print "\t\tLow-threshold TE masking for MAKER gene annotation (masked: $maker_TE): $genome.MAKER.masked\n\n"; + + # copy results out + `cp $genome.MAKER.masked ../`; # make no backup for this file + copy_file("$genome.EDTA.TEanno.gff3", ".."); + copy_file("$genome.EDTA.TEanno.sum", ".."); + copy_file("${genome}_divergence_plot.pdf", ".."); + copy_file("$genome.EDTA.TEanno.density_plots.pdf", ".."); + + # evaluate the annotation consistency + if ($evaluate == 1){ + # report status + chomp ($date = `date`); + print "$date\tEvaluate the level of inconsistency for whole-genome TE annotation:\n\n"; + + # extract whole-genome TE and perform all-v-all blast, then summarize the results + `awk '{if (\$5~/[0-9]+/ && \$1>300 && \$7-\$6>80) print \$11"\t"\$5":"\$6".."\$7}' $genome.EDTA.TEanno.out | perl $call_seq - -C $genome > $genome.EDTA.TE.fa`; + `perl $cleanup_nested -in $genome.EDTA.TE.fa -threads $threads -minlen 80 -miniden 80 -cov 0.95 -blastplus $blastplus -iter 1 -maxcount 100000 2>/dev/null`; + `for i in nested all redun; do perl $count_nested -in $genome.EDTA.TE.fa.stat -cat \$i > $genome.EDTA.TE.fa.stat.\$i.sum; done`; + + # check results and report status + die "ERROR: TE annotation stats results not found in $genome.EDTA.TE.fa.stat!\n\n" unless -s "$genome.EDTA.TE.fa.stat"; + chomp ($date = `date`); + print "$date\tEvaluation of TE annotation finished! Check out these files:\n + Overall: $genome.EDTA.TE.fa.stat.all.sum + Nested: $genome.EDTA.TE.fa.stat.nested.sum + Non-nested: $genome.EDTA.TE.fa.stat.redun.sum\n\n"; + } + + print "\t\tIf you want to learn more about the formatting and information of these files, please visit: + \t\thttps://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A\n\n"; + + } + + +########################## +###### Subroutines ####### +########################## + +sub copy_file { + my ($file, $path) = ($_[0], $_[1]); + # Generate new name with the last modified date and time + my $mod_time = (stat($file))[9]; + my $new_name = $file . "_" . strftime("%Y%m%d_%H%M%S", localtime($mod_time)); + + # resolve symlinks and existing files + if (-l "$path/$file") { + # File is a symbolic link + unlink "$path/$file" or die "ERROR: Failed to remove symbolic link for $path/$file\n\n"; + } elsif (-f "$path/$file") { + # File is a regular file + rename "$path/$file", "$path/$new_name" or die "ERROR: Failed to rename file: $path/$file\n\n"; + } + + # copy file to the path if it's not the current path + `cp $file $path` if abs_path($path) ne abs_path('.'); + } diff --git a/bin/setup_RepeatModeler_postprocess.sh b/bin/setup_RepeatModeler_postprocess.sh index a601979..c015fbe 100755 --- a/bin/setup_RepeatModeler_postprocess.sh +++ b/bin/setup_RepeatModeler_postprocess.sh @@ -18,5 +18,5 @@ EOF sed -n 567,579p "$script_path/EDTA_raw.pl" \ >> input/RepeatModeler_postprocess.pl -sed -n 585,586p "$script_path/EDTA_raw.pl" \ +sed -n 585,584p "$script_path/EDTA_raw.pl" \ >> input/RepeatModeler_postprocess.pl diff --git a/bin/setup_combine_intact_TEs.sh b/bin/setup_combine_intact_TEs.sh new file mode 100755 index 0000000..23e3979 --- /dev/null +++ b/bin/setup_combine_intact_TEs.sh @@ -0,0 +1,14 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > raw/combine_intact_TEs.pl << EOF +my \$genome = 'genome'; +my \$threads = $1; + +my \$bed2gff = "$script_path/bed2gff.pl"; + +EOF + +sed -n 495,504p "$script_path/EDTA.pl" \ + >> raw/combine_intact_TEs.pl \ No newline at end of file diff --git a/bin/setup_final_filter.sh b/bin/setup_final_filter.sh new file mode 100755 index 0000000..53cf715 --- /dev/null +++ b/bin/setup_final_filter.sh @@ -0,0 +1,31 @@ +#!/usr/bin/env bash + +script_path=$(dirname $0) + +cat > final/final_filter.pl << EOF + +my \$genome = 'genome'; +my \$threads = $1; +my \$rm_threads = $1; + +my \$overwrite = 1; + +my \$cleanup_nested = "$script_path/cleanup_nested.pl"; +my \$rename_TE = "$script_path/rename_TE.pl"; +my \$reclassify = "$script_path/classify_by_lib_RM.pl"; +my \$output_by_list = '$script_path/output_by_list.pl'; +my \$rename_by_list = "$script_path/rename_by_list.pl"; +my \$filter_gff = "$script_path/filter_gff3.pl"; +my \$format_gff3 = "$script_path/format_gff3.pl"; +my \$add_id = "$script_path/add_id.pl"; + +my \$blastplus = ''; # Assumed on PATH +my \$repeatmasker = ''; # Assumed on PATH + +EOF + +sed -n 607,612p "$script_path/EDTA.pl" \ + >> final/final_filter.pl + +sed -n 629,676p "$script_path/EDTA.pl" \ + >> final/final_filter.pl diff --git a/conf/modules.config b/conf/modules.config index 82cff15..7e9147f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -13,7 +13,6 @@ process { } withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } publishDir = [ path: { "${params.outdir}/raw/ltr" }, @@ -27,7 +26,6 @@ process { } withName: 'EDTA:ANNOSINE_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } publishDir = [ path: { "${params.outdir}/raw/sine" }, @@ -41,7 +39,6 @@ process { } withName: 'EDTA:REPEATMODELER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } publishDir = [ path: { "${params.outdir}/raw/line" }, @@ -51,7 +48,6 @@ process { } withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } publishDir = [ path: { "${params.outdir}/raw/tir" }, @@ -88,7 +84,6 @@ process { } withName: 'EDTA:HELITRONSCANNER_POSTPROCESS' { - ext.prefix = { "${meta.id}.pp" } publishDir = [ path: { "${params.outdir}/raw/helitron" }, @@ -97,8 +92,18 @@ process { ] } + withName: 'COMBINE_INTACT_TES' { + ext.prefix = { "${meta.id}" } + + publishDir = [ + path: { "${params.outdir}/raw/intact" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: 'EDTA:PROCESS_K' { - ext.prefix = { "${meta.id}.stg1" } + ext.prefix = { "${meta.id}" } publishDir = [ path: { "${params.outdir}/stg1" }, @@ -106,5 +111,15 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: 'EDTA:FINAL_FILTER' { + ext.prefix = { "${meta.id}" } + + publishDir = [ + path: { "${params.outdir}/final" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } \ No newline at end of file diff --git a/modules/local/annosine_postprocess/main.nf b/modules/local/annosine_postprocess/main.nf index 42814ca..29467dc 100644 --- a/modules/local/annosine_postprocess/main.nf +++ b/modules/local/annosine_postprocess/main.nf @@ -12,7 +12,7 @@ process ANNOSINE_POSTPROCESS { path "input/Seed_SINE.fa" output: - tuple val(meta), path('*.SINE.raw.fa') , emit: sine_fa + tuple val(meta), path('*.SINE.fa') , emit: sine_fa path "versions.yml" , emit: versions when: @@ -21,7 +21,6 @@ process ANNOSINE_POSTPROCESS { script: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ setup_AnnoSINE_postprocess.sh \\ $task.cpus @@ -34,7 +33,7 @@ process ANNOSINE_POSTPROCESS { mv \\ input/genome.SINE.raw.fa \\ - ${prefix}.SINE.raw.fa + ${prefix}.SINE.fa cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -48,9 +47,8 @@ process ANNOSINE_POSTPROCESS { stub: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - touch ${prefix}.SINE.raw.fa + touch ${prefix}.SINE.fa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/combine_intact_tes/environment.yml b/modules/local/combine_intact_tes/environment.yml new file mode 100644 index 0000000..6f8a4fc --- /dev/null +++ b/modules/local/combine_intact_tes/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::mdust=2006.10.17 + - bioconda::tesorter=1.4.7 + - bioconda::trf=4.09.1 + - conda-forge::perl=5.32.1 \ No newline at end of file diff --git a/modules/local/combine_intact_tes/main.nf b/modules/local/combine_intact_tes/main.nf new file mode 100644 index 0000000..663d33e --- /dev/null +++ b/modules/local/combine_intact_tes/main.nf @@ -0,0 +1,64 @@ +process COMBINE_INTACT_TES { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cb105ba7d586ab31c1f39feb04c0255a39cc5a55ae7f6ea53f4bf76cdba8a3e5/data': + 'community.wave.seqera.io/library/mdust_tesorter_trf_perl:3424609103d3b065' }" + + input: + tuple val(meta), path(genome, name: 'raw/genome') + path "raw/genome.LTR.intact.raw.fa" + path "raw/genome.LTR.intact.raw.gff3" + path "raw/genome.TIR.intact.raw.fa" + path "raw/genome.TIR.intact.raw.bed" + path "raw/genome.Helitron.intact.raw.fa" + path "raw/genome.Helitron.intact.raw.bed" + + output: + tuple val(meta), path('*.intact.fa') , emit: intact_raw_fa + tuple val(meta), path('*.intact.gff3') , emit: intact_raw_gff + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + setup_combine_intact_TEs.sh \\ + $task.cpus + + cd raw + + perl combine_intact_TEs.pl + + cd - + + mv \\ + raw/genome.EDTA.intact.raw.fa \\ + ${prefix}.intact.fa + + mv \\ + raw/genome.EDTA.intact.raw.gff3 \\ + ${prefix}.intact.gff3 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.intact.fa + touch ${prefix}.intact.gff3 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/final_filter/environment.yml b/modules/local/final_filter/environment.yml new file mode 100644 index 0000000..e03f80c --- /dev/null +++ b/modules/local/final_filter/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::blast=2.16.0 + - bioconda::repeatmasker=4.1.7 \ No newline at end of file diff --git a/modules/local/final_filter/main.nf b/modules/local/final_filter/main.nf new file mode 100644 index 0000000..3f8c1c7 --- /dev/null +++ b/modules/local/final_filter/main.nf @@ -0,0 +1,69 @@ +process FINAL_FILTER { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/91/91c1946f5edb90aa9d2c26eb14e7348f8f4e94dda03bdb2185b72cb3c2d54932/data': + 'community.wave.seqera.io/library/blast_repeatmasker:816962ca420d1d16' }" + + input: + tuple val(meta), path(genome, name: 'final/genome') + path('final/genome.EDTA.raw.fa.cln') + path('final/genome.EDTA.intact.fa.cln2') + path('final/genome.EDTA.intact.raw.gff3') + + output: + tuple val(meta), path('*.intact.fa') , emit: intact_fa + tuple val(meta), path('*.intact.gff3') , emit: intact_gff + tuple val(meta), path('*.TElib.fa') , emit: telib_fa + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + setup_final_filter.sh \\ + $task.cpus + + cd final + + perl final_filter.pl + + cd - + + mv \\ + final/genome.EDTA.intact.fa \\ + ${prefix}.intact.fa + + mv \\ + final/genome.EDTA.intact.gff3 \\ + ${prefix}.intact.gff3 + + mv \\ + final/genome.EDTA.TElib.fa \\ + ${prefix}.TElib.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.intact.fa + touch ${prefix}.intact.gff3 + touch ${prefix}.TElib.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + perl: \$(perl -v | sed -n 's|This is perl.*(\\(.*\\)).*|\\1|p') + repeatmasker: \$(RepeatMasker -v | sed 's/RepeatMasker version //1') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/helitronscanner_postprocess/main.nf b/modules/local/helitronscanner_postprocess/main.nf index d0eb6a3..a1e8b30 100644 --- a/modules/local/helitronscanner_postprocess/main.nf +++ b/modules/local/helitronscanner_postprocess/main.nf @@ -13,10 +13,10 @@ process HELITRONSCANNER_POSTPROCESS { path "input/genome.HelitronScanner.filtered.ext.fa" output: - tuple val(meta), path('*.Helitron.intact.raw.fa.anno.list') , emit: anno_list - tuple val(meta), path('*.Helitron.intact.raw.bed') , emit: raw_bed - tuple val(meta), path('*.Helitron.intact.raw.gff3') , emit: raw_gff - tuple val(meta), path('*.Helitron.intact.raw.fa') , emit: raw_fa + tuple val(meta), path('*.Helitron.intact.anno.list') , emit: anno_list + tuple val(meta), path('*.Helitron.intact.bed') , emit: raw_bed + tuple val(meta), path('*.Helitron.intact.gff3') , emit: raw_gff + tuple val(meta), path('*.Helitron.intact.fa') , emit: raw_fa path "versions.yml" , emit: versions when: @@ -25,7 +25,6 @@ process HELITRONSCANNER_POSTPROCESS { script: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ setup_HelitronScanner_postprocess.sh \\ $task.cpus @@ -38,19 +37,19 @@ process HELITRONSCANNER_POSTPROCESS { mv \\ genome.Helitron.intact.raw.fa.anno.list \\ - ${prefix}.Helitron.intact.raw.fa.anno.list + ${prefix}.Helitron.intact.anno.list mv \\ genome.Helitron.intact.raw.bed \\ - ${prefix}.Helitron.intact.raw.bed + ${prefix}.Helitron.intact.bed mv \\ genome.Helitron.intact.raw.gff3 \\ - ${prefix}.Helitron.intact.raw.gff3 + ${prefix}.Helitron.intact.gff3 mv \\ genome.Helitron.intact.raw.fa \\ - ${prefix}.Helitron.intact.raw.fa + ${prefix}.Helitron.intact.fa cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -64,12 +63,11 @@ process HELITRONSCANNER_POSTPROCESS { stub: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - touch ${prefix}.Helitron.intact.raw.fa.anno.list - touch ${prefix}.Helitron.intact.raw.bed - touch ${prefix}.Helitron.intact.raw.gff3 - touch ${prefix}.Helitron.intact.raw.fa + touch ${prefix}.Helitron.intact.anno.list + touch ${prefix}.Helitron.intact.bed + touch ${prefix}.Helitron.intact.gff3 + touch ${prefix}.Helitron.intact.fa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/ltr_retriever_postprocess/main.nf b/modules/local/ltr_retriever_postprocess/main.nf index e950b59..dd79654 100644 --- a/modules/local/ltr_retriever_postprocess/main.nf +++ b/modules/local/ltr_retriever_postprocess/main.nf @@ -15,10 +15,10 @@ process LTR_RETRIEVER_POSTPROCESS { path "input/genome.LTRlib.fa" output: - tuple val(meta), path('*.LTR.raw.fa') , emit: raw_fa - tuple val(meta), path('*.LTR.intact.raw.fa') , emit: intact_raw_fa - tuple val(meta), path('*.LTR.intact.raw.gff3') , emit: intact_raw_gff3 - tuple val(meta), path('*.LTR.intact.raw.fa.anno.list') , emit: anno_list + tuple val(meta), path('*.LTR.fa') , emit: raw_fa + tuple val(meta), path('*.LTR.intact.fa') , emit: intact_raw_fa + tuple val(meta), path('*.LTR.intact.gff3') , emit: intact_raw_gff3 + tuple val(meta), path('*.LTR.intact.anno.list') , emit: anno_list path "versions.yml" , emit: versions when: @@ -27,7 +27,6 @@ process LTR_RETRIEVER_POSTPROCESS { script: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ setup_LTR_retriever_postprocess.sh \\ $task.cpus @@ -40,19 +39,19 @@ process LTR_RETRIEVER_POSTPROCESS { mv \\ genome.LTR.raw.fa \\ - ${prefix}.LTR.raw.fa + ${prefix}.LTR.fa mv \\ genome.LTR.intact.raw.fa \\ - ${prefix}.genome.LTR.intact.raw.fa + ${prefix}.LTR.intact.fa mv \\ genome.LTR.intact.raw.gff3 \\ - ${prefix}.LTR.intact.raw.gff3 + ${prefix}.LTR.intact.gff3 mv \\ genome.LTR.intact.raw.fa.anno.list \\ - ${prefix}.LTR.intact.raw.fa.anno.list + ${prefix}.LTR.intact.anno.list cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -66,12 +65,11 @@ process LTR_RETRIEVER_POSTPROCESS { stub: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - touch ${prefix}.LTR.raw.fa - touch ${prefix}.genome.LTR.intact.raw.fa - touch ${prefix}.LTR.intact.raw.gff3 - touch ${prefix}.LTR.intact.raw.fa.anno.list + touch ${prefix}.LTR.fa + touch ${prefix}.LTR.intact.fa + touch ${prefix}.LTR.intact.gff3 + touch ${prefix}.LTR.intact.anno.list cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/process_k/main.nf b/modules/local/process_k/main.nf index e385899..dc62ed7 100644 --- a/modules/local/process_k/main.nf +++ b/modules/local/process_k/main.nf @@ -17,16 +17,16 @@ process PROCESS_K { path(helitron , name: "genome.EDTA.raw/genome.Helitron.intact.raw.fa") output: - tuple val(meta), path('*.fasta') , emit: stg1_fa + tuple val(meta), path("${prefix}.fasta"), emit: stg1_fa + tuple val(meta), path('*.intact.fasta') , emit: intact_fa path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: '' - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" def touch_ltr = ltr ? '' : "touch genome.EDTA.raw/genome.LTR.raw.fa" def touch_ltrint = ltrint ? '' : "touch genome.EDTA.raw/genome.LTR.intact.raw.fa" @@ -64,6 +64,10 @@ process PROCESS_K { mv \\ genome.EDTA.combine/genome.EDTA.fa.stg1 \\ ${prefix}.fasta + + mv \\ + genome.EDTA.combine/genome.EDTA.intact.fa.cln \\ + ${prefix}.intact.fasta cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -73,10 +77,10 @@ process PROCESS_K { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.fasta + touch ${prefix}.intact.fasta cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/repeatmodeler_postprocess/main.nf b/modules/local/repeatmodeler_postprocess/main.nf index c1f6459..d79221f 100644 --- a/modules/local/repeatmodeler_postprocess/main.nf +++ b/modules/local/repeatmodeler_postprocess/main.nf @@ -13,7 +13,7 @@ process REPEATMODELER_POSTPROCESS { output: tuple val(meta), path('*.RM2.fa') , emit: rm2_fa - tuple val(meta), path('*.LINE.raw.fa') , emit: line_raw , optional: true + tuple val(meta), path('*.LINE.fa') , emit: line_raw , optional: true path "versions.yml" , emit: versions when: @@ -22,7 +22,6 @@ process REPEATMODELER_POSTPROCESS { script: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ setup_RepeatModeler_postprocess.sh \\ $task.cpus @@ -34,15 +33,13 @@ process REPEATMODELER_POSTPROCESS { cd - mv \\ - genome.RM2.fa \\ + input/genome.RM2.fa \\ ${prefix}.RM2.fa - if [[ -s genome.LINE.raw.fa ]]; then + if [[ -s input/genome.LINE.raw.fa ]]; then mv \\ - genome.LINE.raw.fa \\ - ${prefix}.LINE.raw.fa - else - rm genome.LINE.raw.fa + input/genome.LINE.raw.fa \\ + ${prefix}.LINE.fa fi cat <<-END_VERSIONS > versions.yml @@ -57,7 +54,6 @@ process REPEATMODELER_POSTPROCESS { stub: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.RM2.fa diff --git a/modules/local/tir_learner_postprocess/main.nf b/modules/local/tir_learner_postprocess/main.nf index 275fc5a..d4001db 100644 --- a/modules/local/tir_learner_postprocess/main.nf +++ b/modules/local/tir_learner_postprocess/main.nf @@ -13,9 +13,9 @@ process TIR_LEARNER_POSTPROCESS { path "input/TIR-Learner-Result/TIR-Learner_FinalAnn.gff3" output: - tuple val(meta), path('*.TIR.intact.raw.fa') , emit: intact_raw_fa - tuple val(meta), path('*.TIR.intact.raw.gff3') , emit: intact_raw_gff3 - tuple val(meta), path('*.TIR.intact.raw.bed') , emit: intact_raw_bed + tuple val(meta), path('*.TIR.intact.fa') , emit: intact_raw_fa + tuple val(meta), path('*.TIR.intact.gff3') , emit: intact_raw_gff3 + tuple val(meta), path('*.TIR.intact.bed') , emit: intact_raw_bed path "versions.yml" , emit: versions when: @@ -24,7 +24,6 @@ process TIR_LEARNER_POSTPROCESS { script: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ setup_TIR-Learner_postprocess.sh \\ $task.cpus @@ -37,15 +36,15 @@ process TIR_LEARNER_POSTPROCESS { mv \\ genome.TIR.intact.raw.fa \\ - ${prefix}.TIR.intact.raw.fa + ${prefix}.TIR.intact.fa mv \\ genome.TIR.intact.raw.gff3 \\ - ${prefix}.TIR.intact.raw.gff3 + ${prefix}.TIR.intact.gff3 mv \\ genome.TIR.intact.raw.bed \\ - ${prefix}.TIR.intact.raw.bed + ${prefix}.TIR.intact.bed cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -59,11 +58,10 @@ process TIR_LEARNER_POSTPROCESS { stub: def prefix = task.ext.prefix ?: "${meta.id}" def MDUST_VERSION = '2006.10.17' // WARN: Manually update when changing Bioconda assets - if ( "$prefix" == 'genome' ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - touch ${prefix}.TIR.intact.raw.fa - touch ${prefix}.TIR.intact.raw.gff3 - touch ${prefix}.TIR.intact.raw.bed + touch ${prefix}.TIR.intact.fa + touch ${prefix}.TIR.intact.gff3 + touch ${prefix}.TIR.intact.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index e293c39..43e207c 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -19,16 +19,18 @@ nextflow_pipeline { false, [ 'pipeline_info/*.{html,json,txt,yml}', - 'raw/ltr/*.pp.LTR.intact.raw.gff3', - 'raw/ltr/*.pp.LTR.raw.fa', - 'raw/tir/*.pp.TIR.intact.raw.fa', - 'raw/tir/*.pp.TIR.intact.raw.gff3', - 'raw/line/*.pp.LINE.raw.fa', - 'raw/line/*.pp.RM2.fa', - 'raw/helitron/*.Helitron.intact.raw.fa', - 'raw/helitron/*.Helitron.intact.raw.fa.anno.list', - 'raw/helitron/*.Helitron.intact.raw.gff3', - 'stg1/*.stg1.fasta' + 'raw/ltr/*.LTR.intact.gff3', + 'raw/ltr/*.LTR.fa', + 'raw/tir/*.TIR.intact.fa', + 'raw/tir/*.TIR.intact.gff3', + 'raw/line/*.LINE.fa', + 'raw/line/*.RM2.fa', + 'raw/helitron/*.Helitron.intact.fa', + 'raw/helitron/*.Helitron.intact.anno.list', + 'raw/helitron/*.Helitron.intact.gff3', + 'raw/intact/*', + 'stg1/*.fasta', + 'final/*' ], null, ['**'] diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index 8bd6b84..dccc812 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -2,7 +2,7 @@ "small genome": { "content": [ { - "successful tasks": 22, + "successful tasks": 24, "versions": { "ANNOSINE": { "annosine": "2.0.7" @@ -10,6 +10,13 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "COMBINE_INTACT_TES": { + "perl": "v5.32.1" + }, + "FINAL_FILTER": { + "perl": "v5.32.1", + "repeatmasker": "4.1.7-p1" + }, "FORMAT_HELITRONSCANNER_OUT": { "perl": "v5.32.1" }, @@ -87,32 +94,40 @@ } }, "stable paths": [ - "genome.pp.Helitron.intact.raw.bed:md5,a8b170a1ee8d36c7f8e3af5ba1e43cb6", - "genome.pp.LTR.intact.raw.fa.anno.list:md5,51261f020350b448acdf89d8fb625448", - "genome.pp.genome.LTR.intact.raw.fa:md5,ae2336f498897d1af4e8d3be28bb3f25", - "genome.pp.TIR.intact.raw.bed:md5,12406184046b11edc2ddadbc82765966" + "genome.Helitron.intact.bed:md5,a8b170a1ee8d36c7f8e3af5ba1e43cb6", + "genome.LTR.intact.anno.list:md5,51261f020350b448acdf89d8fb625448", + "genome.LTR.intact.fa:md5,ae2336f498897d1af4e8d3be28bb3f25", + "genome.TIR.intact.bed:md5,12406184046b11edc2ddadbc82765966" ], "stable names": [ + "final", + "final/genome.TElib.fa", + "final/genome.intact.fa", + "final/genome.intact.gff3", "pipeline_info", "raw", "raw/helitron", - "raw/helitron/genome.pp.Helitron.intact.raw.bed", - "raw/helitron/genome.pp.Helitron.intact.raw.fa", - "raw/helitron/genome.pp.Helitron.intact.raw.fa.anno.list", - "raw/helitron/genome.pp.Helitron.intact.raw.gff3", + "raw/helitron/genome.Helitron.intact.anno.list", + "raw/helitron/genome.Helitron.intact.bed", + "raw/helitron/genome.Helitron.intact.fa", + "raw/helitron/genome.Helitron.intact.gff3", + "raw/intact", + "raw/intact/genome.intact.fa", + "raw/intact/genome.intact.gff3", "raw/line", - "raw/line/genome.pp.RM2.fa", + "raw/line/genome.RM2.fa", "raw/ltr", - "raw/ltr/genome.pp.LTR.intact.raw.fa.anno.list", - "raw/ltr/genome.pp.LTR.intact.raw.gff3", - "raw/ltr/genome.pp.LTR.raw.fa", - "raw/ltr/genome.pp.genome.LTR.intact.raw.fa", + "raw/ltr/genome.LTR.fa", + "raw/ltr/genome.LTR.intact.anno.list", + "raw/ltr/genome.LTR.intact.fa", + "raw/ltr/genome.LTR.intact.gff3", "raw/tir", - "raw/tir/genome.pp.TIR.intact.raw.bed", - "raw/tir/genome.pp.TIR.intact.raw.fa", - "raw/tir/genome.pp.TIR.intact.raw.gff3", + "raw/tir/genome.TIR.intact.bed", + "raw/tir/genome.TIR.intact.fa", + "raw/tir/genome.TIR.intact.gff3", "stg1", - "stg1/genome.stg1.fasta" + "stg1/genome.fasta", + "stg1/genome.intact.fasta" ] } ], @@ -120,6 +135,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-13T15:35:15.109085" + "timestamp": "2024-12-17T14:02:22.882318" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index 70d70de..1f13998 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -21,7 +21,9 @@ include { FORMAT_HELITRONSCANNER_OUT } from '../modules/local/for include { FORMAT_HELITRONSCANNER_OUT as FORMAT_HELITRONSCANNER_OUT_EXT } from '../modules/local/format_helitronscanner_out/main' include { HELITRONSCANNER_POSTPROCESS } from '../modules/local/helitronscanner_postprocess/main' +include { COMBINE_INTACT_TES } from '../modules/local/combine_intact_tes/main' include { PROCESS_K } from '../modules/local/process_k/main' +include { FINAL_FILTER } from '../modules/local/final_filter/main' include { softwareVersionsToYAML } from '../modules/local/utils/main' include { idFromFileName } from '../modules/local/utils/main' @@ -251,6 +253,36 @@ workflow EDTA { ch_versions = ch_versions.mix(HELITRONSCANNER_POSTPROCESS.out.versions.first()) + // MODULE: COMBINE_INTACT_TES + ch_combine_intact_tes_inputs = ch_sanitized_fasta + | join ( LTR_RETRIEVER_POSTPROCESS.out.intact_raw_fa ) + | join ( LTR_RETRIEVER_POSTPROCESS.out.intact_raw_gff3 ) + | join ( TIR_LEARNER_POSTPROCESS.out.intact_raw_fa ) + | join ( TIR_LEARNER_POSTPROCESS.out.intact_raw_bed ) + | join ( HELITRONSCANNER_POSTPROCESS.out.raw_fa ) + | join ( HELITRONSCANNER_POSTPROCESS.out.raw_bed ) + | multiMap { meta, genome, ltr_fa, ltr_gff, tir_fa, tir_bed, helitron_fa, helitron_bed -> + genome : [ meta, genome ] + ltr_fa : ltr_fa + ltr_gff : ltr_gff + tir_fa : tir_fa + tir_bed : tir_bed + helitron_fa : helitron_fa + helitron_bed: helitron_bed + } + + COMBINE_INTACT_TES ( + ch_combine_intact_tes_inputs.genome, + ch_combine_intact_tes_inputs.ltr_fa, + ch_combine_intact_tes_inputs.ltr_gff, + ch_combine_intact_tes_inputs.tir_fa, + ch_combine_intact_tes_inputs.tir_bed, + ch_combine_intact_tes_inputs.helitron_fa, + ch_combine_intact_tes_inputs.helitron_bed, + ) + + ch_versions = ch_versions.mix(COMBINE_INTACT_TES.out.versions.first()) + // MODULE: PROCESS_K ch_process_k_inputs = ch_sanitized_fasta | join ( LTR_RETRIEVER_POSTPROCESS.out.raw_fa ) @@ -294,6 +326,26 @@ workflow EDTA { } } + // MODULE: FINAL_FILTER + ch_final_filter_inputs = ch_sanitized_fasta + | join(PROCESS_K.out.stg1_fa) + | join(PROCESS_K.out.intact_fa) + | join(COMBINE_INTACT_TES.out.intact_raw_gff) + | multiMap { meta, fasta, stg1_fa, intact_fa, intact_gff -> + genome : [ meta, fasta ] + stg1_fa : stg1_fa + intact_fa : intact_fa + intact_gff : intact_gff + } + FINAL_FILTER ( + ch_final_filter_inputs.genome, + ch_final_filter_inputs.stg1_fa, + ch_final_filter_inputs.intact_fa, + ch_final_filter_inputs.intact_gff, + ) + + ch_versions = ch_versions.mix(FINAL_FILTER.out.versions.first()) + // Function: Save versions ch_versions = ch_versions | unique From ecdaccf2d1961612da3c3263966dd2b5033146f5 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 17 Dec 2024 22:38:50 +1300 Subject: [PATCH 45/49] Updated the sanitize process --- bin/fffx | Bin 1555504 -> 0 bytes conf/modules.config | 80 ++---- conf/test.config | 6 +- modules.json | 12 +- .../custom/restoregffids/environment.yml | 6 + modules/gallvp/custom/restoregffids/main.nf | 35 +++ modules/gallvp/custom/restoregffids/meta.yml | 60 +++++ .../templates/restore_gff_ids.py | 47 ++++ .../custom/restoregffids/tests/main.nf.test | 63 +++++ .../restoregffids/tests/main.nf.test.snap | 61 +++++ .../custom/shortenfastaids/environment.yml | 7 + modules/gallvp/custom/shortenfastaids/main.nf | 38 +++ .../gallvp/custom/shortenfastaids/meta.yml | 66 +++++ .../templates/shorten_fasta_ids.py | 168 +++++++++++++ .../custom/shortenfastaids/tests/main.nf.test | 123 ++++++++++ .../shortenfastaids/tests/main.nf.test.snap | 227 ++++++++++++++++++ modules/gallvp/tirlearner/main.nf | 5 +- .../gallvp/tirlearner/tests/main.nf.test.snap | 20 +- modules/local/sanitize/main.nf | 38 --- tests/nf-test/small/main.nf.test | 26 +- tests/nf-test/small/main.nf.test.snap | 47 +--- tests/nf-test/tiny/main.nf.test | 6 +- tests/nf-test/tiny/main.nf.test.snap | 15 +- workflows/edta.nf | 58 ++++- 24 files changed, 1039 insertions(+), 175 deletions(-) delete mode 100755 bin/fffx create mode 100644 modules/gallvp/custom/restoregffids/environment.yml create mode 100644 modules/gallvp/custom/restoregffids/main.nf create mode 100644 modules/gallvp/custom/restoregffids/meta.yml create mode 100755 modules/gallvp/custom/restoregffids/templates/restore_gff_ids.py create mode 100644 modules/gallvp/custom/restoregffids/tests/main.nf.test create mode 100644 modules/gallvp/custom/restoregffids/tests/main.nf.test.snap create mode 100644 modules/gallvp/custom/shortenfastaids/environment.yml create mode 100644 modules/gallvp/custom/shortenfastaids/main.nf create mode 100644 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${group}

\n" + summary_section += "
\n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
${param}
${group_params.get(param) ?: 'N/A'}
\n" + } + summary_section += "
\n" + } + } + + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + def colorcodes = [:] as Map + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() + } + } else { + return null + } +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" + if (!workflow.success) { + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" + } + + def summary = [:] + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = getSingleReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + def colors = logColours(monochrome_logs) as Map + if (email_address) { + try { + if (plaintext_email) { + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") + // Catch failures and try with plaintext + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] + mail_cmd.execute() << email_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + def colors = logColours(monochrome_logs) as Map + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") + } + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection() + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 0000000..d08d243 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 0000000..f117040 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,126 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function getSingleReport with a single file") { + function "getSingleReport" + + when { + function { + """ + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert function.result.contains("test.tsv") } + ) + } + } + + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" + + when { + function { + """ + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 0000000..02c6701 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,136 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 0000000..8940d32 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 0000000..859d103 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 0000000..d0a926b --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 0000000..ac8523c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000..4994303 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000..f7d9f02 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 0000000..8fb3016 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000..0907ac5 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json new file mode 100644 index 0000000..331e0d2 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "$defs": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_output_options" + }, + { + "$ref": "#/$defs/generic_options" + } + ] +} diff --git a/workflows/edta.nf b/workflows/edta.nf index 1d9bb26..97b91fd 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -27,24 +27,20 @@ include { COMBINE_INTACT_TES } from '../modules/local/com include { PROCESS_K } from '../modules/local/process_k/main' include { FINAL_FILTER } from '../modules/local/final_filter/main' -include { softwareVersionsToYAML } from '../modules/local/utils/main' -include { idFromFileName } from '../modules/local/utils/main' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline/main' workflow EDTA { + take: + ch_genome_gz // Channel: < val(meta), path(fasta|fasta.gz) > + main: // Versions channel ch_versions = Channel.empty() - ch_genome_branch = Channel.fromPath(params.genome) - | map { genome -> - def meta = [:] - meta.id = idFromFileName ( genome.baseName ) - - [ meta, genome ] - } + ch_genome_branch = ch_genome_gz | branch { _meta, archive -> gz: "$archive".endsWith('.gz') rest: ! "$archive".endsWith('.gz') From ac93561de5adab542b0cdc9ea725bc7303a33cfb Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 18 Dec 2024 11:21:04 +1300 Subject: [PATCH 47/49] Added pre-commit hook for version check --- .github/version_checks.sh | 11 +++++++++++ .pre-commit-config.yaml | 8 ++++++++ nextflow.config | 2 +- 3 files changed, 20 insertions(+), 1 deletion(-) create mode 100755 .github/version_checks.sh diff --git a/.github/version_checks.sh b/.github/version_checks.sh new file mode 100755 index 0000000..a49deef --- /dev/null +++ b/.github/version_checks.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +set -euo pipefail + +config_version=$(sed -n "/^\s*version\s*=\s*'/s/version//p" nextflow.config | tr -d "=[:space:]'") +perl_version=$(sed -n 's|^my $version = "\(.*\)";|\1|p' EDTA.pl | tr -d '[:space:]') + +if [[ "v$config_version" != $perl_version ]]; then + echo "config_version (v$config_version) != perl_version ($perl_version)" + exit 1 +fi diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 650f6a9..c559076 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,3 +9,11 @@ repos: always_run: true fail_fast: true pass_filenames: false + - id: version_checks + name: Version checks + language: system + entry: > + .github/version_checks.sh + always_run: true + fail_fast: true + pass_filenames: false diff --git a/nextflow.config b/nextflow.config index c9c7aa1..8f8fd40 100644 --- a/nextflow.config +++ b/nextflow.config @@ -173,7 +173,7 @@ dag { manifest { name = 'oushujun/EDTA' description = 'Extensive de-novo TE Annotator' - version = '3.0.0dev' + version = '2.2.2' nextflowVersion = '!>=24.10.3' contributors = [ [ From 8e48bd5446a03fa0bb875dd6c8451c3e7634ea4b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 18 Dec 2024 11:27:48 +1300 Subject: [PATCH 48/49] Updated snapshots --- .github/workflows/ci.yml | 2 +- tests/nf-test/small/main.nf.test.snap | 6 +++--- tests/nf-test/tiny/main.nf.test.snap | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3a33d22..05fa7bd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,7 +72,7 @@ jobs: - uses: nf-core/setup-nf-test@v1.1.2 with: - version: 0.9.0 + version: 0.9.2 - name: Setup apptainer if: matrix.profile == 'singularity' diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index 06527a9..676abd8 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -94,7 +94,7 @@ "mdust": "2006.10.17" }, "Workflow": { - "oushujun/EDTA": "v0.1.0dev" + "oushujun/EDTA": "v2.2.2" } }, "stable paths": [ @@ -112,8 +112,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.04.4" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T22:28:58.604502" + "timestamp": "2024-12-18T11:26:59.305705" } } \ No newline at end of file diff --git a/tests/nf-test/tiny/main.nf.test.snap b/tests/nf-test/tiny/main.nf.test.snap index 40e5592..c224e45 100644 --- a/tests/nf-test/tiny/main.nf.test.snap +++ b/tests/nf-test/tiny/main.nf.test.snap @@ -53,7 +53,7 @@ "TIR-Learner": "v3.0.2" }, "Workflow": { - "oushujun/EDTA": "v0.1.0dev" + "oushujun/EDTA": "v2.2.2" } }, "stable paths": [ @@ -68,8 +68,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.04.4" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-17T17:06:09.728972" + "timestamp": "2024-12-18T11:22:27.159514" } } \ No newline at end of file From c5098279c5213bdf782c3e70f263d422fd573547 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 18 Dec 2024 17:02:35 +1300 Subject: [PATCH 49/49] Updated README --- README.md | 92 +++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 63 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index 5aff5d4..b0523b3 100644 --- a/README.md +++ b/README.md @@ -1,29 +1,34 @@ [![install with bioconda](https://anaconda.org/bioconda/edta/badges/platforms.svg)](https://anaconda.org/bioconda/edta) [![Anaconda-Server Badge](https://anaconda.org/bioconda/edta/badges/license.svg)](https://github.com/oushujun/EDTA/blob/master/LICENSE) [![Anaconda-Server Badge](https://anaconda.org/bioconda/edta/badges/version.svg)](https://anaconda.org/bioconda/edta) [![Anaconda-Server Badge](https://anaconda.org/bioconda/edta/badges/downloads.svg)](https://anaconda.org/bioconda/edta) - -# The Extensive *de novo* TE Annotator (EDTA) - -## Table of Contents - - * [Introduction](#introduction) - * [Installation](#installation) - * [Quick installation using conda/mamba](#install-with-condamamba-linux64) - * [Quick installation using Singularity](#install-with-singularity-good-for-hpc-users) - * [Quick installation using Docker](#install-with-docker-good-for-rootmacosapple-m-chip-users) - * [Testing](#testing) - * [Inputs](#inputs) - * [Outputs](#outputs) - * [EDTA usage](#edta-usage) - * [From head to toe](#from-head-to-toe) - * [Divide and conquer](#divide-and-conquer) - * [Protips and self-diagnosis](#protips-and-self-diagnosis) - * [panEDTA usage](#panedta-usage) - * [Benchmark](#benchmark) - * [Citations](#citations) - * [Other resources](#other-resources) - * [Questions and Issues](#questions-and-issues) - * [Acknowledgements](#acknowledgements) - +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.3-23aa62.svg)](https://www.nextflow.io/) +[![run with conda](http://img.shields.io/badge/run%20with-conda%20-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) + +# The Extensive *de novo* TE Annotator (EDTA) + +## Table of Contents + +- [Introduction](#introduction) +- [Installation](#installation) + - [Install with conda/mamba (Linux64)](#install-with-condamamba-linux64) + - [Install with Singularity (good for HPC users)](#install-with-singularity-good-for-hpc-users) + - [Install with Docker (good for root/macOS/Apple M-chip users)](#install-with-docker-good-for-rootmacosapple-m-chip-users) +- [Testing](#testing) +- [Inputs](#inputs) +- [Outputs](#outputs) +- [EDTA Usage](#edta-usage) + - [From head to toe](#from-head-to-toe) + - [Divide and conquer](#divide-and-conquer) + - [Protips and self-diagnosis](#protips-and-self-diagnosis) + - [Run with Nextflow](#run-with-nextflow) +- [panEDTA usage](#panedta-usage) +- [Benchmark](#benchmark) +- [Citations](#citations) +- [Other resources](#other-resources) +- [Questions and Issues](#questions-and-issues) +- [Acknowledgements](#acknowledgements) ## Introduction This package is developed for automated whole-genome *de-novo* TE annotation and benchmarking the annotation performance of TE libraries. @@ -41,7 +46,6 @@ To benchmark the annotation quality of a new library/method, I have provided the For pan-genome annotations, you need to annotate each genome with EDTA, generate a pan-genome library, then reannotate each genome with the pan-genome library. Please refer to this [example](https://github.com/HuffordLab/NAM-genomes/tree/master/te-annotation) for details. A sequential version of panEDTA is also included in this package. - ## Installation There are several ways to install EDTA. You just need to find the one that works for your system. If you are not using macOS, you may try the conda approach before the Singularity approach. @@ -120,8 +124,8 @@ Visit [BioContainers](https://quay.io/repository/biocontainers/edta?tab=tags) re Note: Because only the current directory is mounted to the EDTA docker container, you have to copy all needed files to the current directory and provide them to EDTA without path specifications. Even providing the absolute path to the file located in this folder won't work. Softlinked files are considered "with path" and won't work. Similarily, specifying your own versions of dependency programs (i.e., repeatmasker, repeatmodeler) won't work because they have paths. - ## Testing + You should test the EDTA pipeline with a 1-Mb toy genome, which takes about five mins. If your test finishs without any errors (warnings are OK), then EDTA should be correctly installed. If the test is OK but you encounter errors with your data, you should check your own data for any formating/naming mistakes. ``` @@ -131,8 +135,8 @@ perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/ If your test fails, you may check out this [collection of issues](https://github.com/oushujun/EDTA/wiki/Installations,-builds,-and-tests-Q&A) for possible reasons and solutions. If none works, you may open a new issue. - ## Inputs + Required: The genome file [FASTA]. Please make sure sequence names are short (<=13 characters) and simple (i.e, letters, numbers, and underscore). Optional: @@ -140,8 +144,8 @@ Optional: 2. Known gene positions of this version of the genome assembly [BED]. Coordinates specified in this file will be excluded from TE annotation to avoid over-masking. 3. Curated TE library of the species [FASTA]. This file is trusted 100%. Please make sure it's curated. If you only have a couple of curated sequences, that's also good. It doesn't need to be complete. Providing curated TE sequences, especially for those under-annotated TE types (i.e., SINEs and LINEs), will greatly improve the annotation quality. For more information, please visit this wiki page: [How to prepare a curated library to maximize the efficacy of EDTA](https://github.com/oushujun/EDTA/wiki/How-to-prepare-a-curated-library-to-maximize-the-efficacy-of-EDTA) - ## Outputs + A non-redundant TE library: $genome.mod.EDTA.TElib.fa. The curated library will be included in this file if provided. The [rice library](./database/rice7.0.0.liban) will be (partially) included if `--force 1` is specified. TEs are classified into the superfamily level and using the three-letter naming system reported in [Wicker et al. (2007)](https://www.nature.com/articles/nrg2165). Each sequence can be considered as a TE family. To convert between classification systems, please refer to the [TE sequence ontology file](./bin/TE_Sequence_Ontology.txt). Optional 1: @@ -155,10 +159,10 @@ Optional 2, when you specify the `--anno 1` parameter, you will get: 6. Annotation inconsistency for nested TEs: $genome.mod.EDTA.TE.fa.stat.nested.sum. 7. Oveall annotation inconsistency: $genome.mod.EDTA.TE.fa.stat.all.sum. - ## EDTA Usage ### From head to toe + *You got a genome and you want to get a high-quality TE annotation:* perl EDTA.pl [options] @@ -189,6 +193,7 @@ Optional 2, when you specify the `--anno 1` parameter, you will get: --help|-h Display this help info ### Divide and conquer + *Identify intact elements of a paticular TE type*: 1.Get raw TEs from a genome (specify `-type ltr|tir|helitron` in different runs) @@ -207,11 +212,35 @@ Optional 2, when you specify the `--anno 1` parameter, you will get: perl EDTA.pl --overwrite 0 [options] ### Protips and self-diagnosis + 1. It's never said enough. You should tidy up all your sequence names before ANY analysis. Keep them short, simple, and unique. 2. Run it in a fast drive (i.e., SSD) because RepeatMasker/RepeatModeler is I/O intense. 3. Check out the [Wiki page](https://github.com/oushujun/EDTA/wiki) for more information and frequently asked questions. +### Run with [Nextflow](https://www.nextflow.io/) + +A limited beta version of the pipeline implemented in Nextflow is also available. The pipeline can be launched with Nextflow without the need to download it. Nextflow takes care of the pipeline download and dependency setup through the chosen execution engine such as Docker, Singularity, Conda, Mamba, Podman, etc. + +```bash +nextflow run oushujun/EDTA \ + -revision \ + -profile \ + --genome \ + --outdir +``` + +Where, `--genome` is either a path to a fasta file or a text file which lists fasta files, and `--outdir` is a path to a directory where the pipeline outputs should be stored. + +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. For example when using Conda for dependency management, make sure Conda is installed and then test the pipeline on the included test data with, + +```bash +nextflow run oushujun/EDTA \ + -profile conda,test + --outdir results +``` + ## panEDTA usage + This is the serial version of panEDTA. Each genome will be annotated sequentially and then combined with the panEDTA functionality. Existing EDTA annotation of genomes (EDTA run with --anno 1) will be recognized and reused. A way to acclerate the pan-genome annotation is to execute EDTA annotation of each genomes separately and in parallel, then execute panEDTA to finish the remaining of the runs. You may want to save the GFF files and the sum file of the EDTA results of each genome because they will be overwritten by panEDTA. To help filtering out gene-related sequences, at least one CDS file is required. Please read [wiki](https://github.com/oushujun/EDTA/wiki/Making-sense-of-EDTA-usage-and-outputs---Q&A) for the CDS requirement. You may want to check out the toy example in the ./test folder to get familiarized. sh panEDTA.sh -g genome_list.txt -c cds.fasta -t 10 @@ -231,6 +260,7 @@ This is the serial version of panEDTA. Each genome will be annotated sequentiall ## Benchmark + If you developed a new TE method/got a TE library and want to compare it's annotation performance to the methods we have tested, you can: 1.annotate the rice genome with your test library: @@ -256,6 +286,7 @@ eg. Note: the -std and -tst files should be named differently even they are placed in different folders. ## Citations + Please cite our paper if you find EDTA useful: Ou S., Su W., Liao Y., Chougule K., Agda J. R. A., Hellinga A. J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. [Genome Biol. 20(1): 275.](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y) @@ -267,10 +298,13 @@ Ou S., Collins T., Qiu Y., Seetharam A., Menard C., Manchanda N., Gent J., Schat Please also cite the software packages that were used in EDTA, listed in the [EDTA/bin](./bin) directory. ## Other resources + You may download the [rice genome here](http://rice.uga.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/) (the "all.con" file). ## Questions and Issues + You may want to check out this [Q&A page](https://github.com/oushujun/EDTA/wiki) for best practices and get answered. If you have other issues with installation and usage, please check if similar issues have been reported in [Issues](https://github.com/oushujun/EDTA/issues) or open a new issue. If you are (looking for) happy users, please read or write successful cases [here](https://github.com/oushujun/EDTA/issues/15). ## Acknowledgements + I want to thank [Jacques Dainat](https://github.com/Juke34) for contribution of the EDTA conda recipe as well as improving the codes. I also want to thank [Qiushi Li](https://github.com/QiushiLi), [Zhigui Bao](https://github.com/baozg), [Philipp Bayer](https://github.com/philippbayer), [Nick Carleson](https://github.com/Neato-Nick), [@aderzelle](https://github.com/aderzelle), [Sanzhen Liu](https://github.com/liu3zhenlab), [Zhougeng Xu](https://github.com/xuzhougeng), [Shun Wang](https://github.com/wangshun1121), [Nancy Manchanda](https://github.com/nm100), [Eric Burgueño](https://github.com/eburgueno), [Sergei Ryazansky](https://github.com/DrHogart), and many more others for testing, debugging, and improving the EDTA pipeline.

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ext.args = '-size 1000000 -time 300' ext.prefix = { "${meta.id}_ltrharvest" } @@ -12,48 +21,17 @@ process { ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } } - withName: 'EDTA:LTR_RETRIEVER_POSTPROCESS' { - - publishDir = [ - path: { "${params.outdir}/raw/ltr" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: 'EDTA:ANNOSINE' { + ext.prefix = { "${meta.id}.annosine" } ext.args = params.annosine_ext_args ?: '-a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' } - withName: 'EDTA:ANNOSINE_POSTPROCESS' { - - publishDir = [ - path: { "${params.outdir}/raw/sine" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: 'EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' } - withName: 'EDTA:REPEATMODELER_POSTPROCESS' { - - publishDir = [ - path: { "${params.outdir}/raw/line" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'EDTA:TIR_LEARNER_POSTPROCESS' { - - publishDir = [ - path: { "${params.outdir}/raw/tir" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] + withName: 'EDTA:TIRLEARNER' { + ext.prefix = { "${meta.id}.tirlearner" } } withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { @@ -83,40 +61,24 @@ process { ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' } - withName: 'EDTA:HELITRONSCANNER_POSTPROCESS' { - + withName: 'EDTA:FINAL_FILTER' { publishDir = [ - path: { "${params.outdir}/raw/helitron" }, + path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'COMBINE_INTACT_TES' { - ext.prefix = { "${meta.id}" } + saveAs: { filename -> - publishDir = [ - path: { "${params.outdir}/raw/intact" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } + if ( filename.equals('versions.yml') ) { return null } - withName: 'EDTA:PROCESS_K' { - ext.prefix = { "${meta.id}" } + if ( filename.endsWith('gff3') && meta.changed_ids ) { return null } - publishDir = [ - path: { "${params.outdir}/stg1" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + filename + } ] } - withName: 'EDTA:FINAL_FILTER' { - ext.prefix = { "${meta.id}" } - + withName: 'EDTA:CUSTOM_RESTOREGFFIDS' { publishDir = [ - path: { "${params.outdir}/final" }, + path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/conf/test.config b/conf/test.config index 7f76e47..6d0509d 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,9 +1,5 @@ params { - genome = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz' - - // Following parameters for ANNOSINE are not recommended. - // These are used here with the test data to produce testable outputs - annosine_ext_args = '-a 2 -rpm 0 --copy_number 1 --shift 200' + genome = 'https://raw.githubusercontent.com/oushujun/EDTA/4f0424b8a3ce2caccdd51b4021c61a536fa9ead9/test/genome.fa' } process { diff --git a/modules.json b/modules.json index 5d34d4e..b012c3e 100644 --- a/modules.json +++ b/modules.json @@ -10,6 +10,16 @@ "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] }, + "custom/restoregffids": { + "branch": "main", + "git_sha": "072113038b5591f8244ce76b2c9dd8100c912b18", + "installed_by": ["modules"] + }, + "custom/shortenfastaids": { + "branch": "main", + "git_sha": "072113038b5591f8244ce76b2c9dd8100c912b18", + "installed_by": ["modules"] + }, "gunzip": { "branch": "main", "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", @@ -27,7 +37,7 @@ }, "tirlearner": { "branch": "main", - "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", + "git_sha": "072113038b5591f8244ce76b2c9dd8100c912b18", "installed_by": ["modules"] } } diff --git a/modules/gallvp/custom/restoregffids/environment.yml b/modules/gallvp/custom/restoregffids/environment.yml new file mode 100644 index 0000000..68eaa88 --- /dev/null +++ b/modules/gallvp/custom/restoregffids/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - "python=3.10.2" diff --git a/modules/gallvp/custom/restoregffids/main.nf b/modules/gallvp/custom/restoregffids/main.nf new file mode 100644 index 0000000..39c8fde --- /dev/null +++ b/modules/gallvp/custom/restoregffids/main.nf @@ -0,0 +1,35 @@ +process CUSTOM_RESTOREGFFIDS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.10.2': + 'biocontainers/python:3.10.2' }" + + input: + tuple val(meta), path(gff3) + path(ids_tsv) + + output: + tuple val(meta), path("*.restored.ids.gff3") , emit: restored_ids_gff3 + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + template 'restore_gff_ids.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.restored.ids.gff3" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | cut -d' ' -f2) + END_VERSIONS + """ +} diff --git a/modules/gallvp/custom/restoregffids/meta.yml b/modules/gallvp/custom/restoregffids/meta.yml new file mode 100644 index 0000000..dea7577 --- /dev/null +++ b/modules/gallvp/custom/restoregffids/meta.yml @@ -0,0 +1,60 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_restoregffids" +description: | + Restores IDs in a gff3 file based on a TSV table + consisting of original (first column) and new IDs (second column). + This module is helpful when some tools like EDTA implicitly shorten + the IDs without producing the ID map, leading to downstream mismatch + in IDs across files. +keywords: + - genome + - gff + - ID + - shorten + - restore +tools: + - "python": + description: | + Python is a programming language that lets you work quickly + and integrate systems more effectively + homepage: "https://www.python.org" + documentation: "https://docs.python.org/3/" + tool_dev_url: "https://github.com/python/cpython" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" + - - ids_tsv: + type: file + description: | + A TSV file with original (first column) and new ids (second column) + if id change was required + pattern: "*.tsv" +output: + - restored_ids_gff3: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.restored.ids.gff3": + type: file + description: GFF3 file with restored ids + pattern: "*.restored.ids.gff3" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/custom/restoregffids/templates/restore_gff_ids.py b/modules/gallvp/custom/restoregffids/templates/restore_gff_ids.py new file mode 100755 index 0000000..2bde7ab --- /dev/null +++ b/modules/gallvp/custom/restoregffids/templates/restore_gff_ids.py @@ -0,0 +1,47 @@ +#!/usr/bin/env python3 + +from platform import python_version + +ids_tsv = "$ids_tsv" +input_gff3 = "$gff3" +output_prefix = "$prefix" + + +def create_name_mapping_from_tsv(file_path): + dictionary = {} + + with open(file_path) as tsv_file: + for line in tsv_file: + columns = line.strip().split("\\t") + if len(columns) != 2: + raise ValueError(f"{file_path} should be a two column TSV file") + + orig_id, new_id = columns[0], columns[1] + dictionary[new_id] = orig_id + + return dictionary + + +def restore_gff3_ids(new_to_orig_ids, file_path, output_file_name): + # Write versions + with open("versions.yml", "w") as f_versions: + f_versions.write('"${task.process}":\\n') + f_versions.write(f" python: {python_version()}\\n") + + with open(file_path) as input_gff3_file: + input_lines = input_gff3_file.readlines() + + with open(output_file_name, "w") as output_gff_file: + for line in input_lines: + if line.startswith("##"): + output_gff_file.write(line) + continue + + new_id = line.split("\\t")[0] + orig_id = new_to_orig_ids[new_id] + output_gff_file.write("\\t".join([orig_id] + line.split("\\t")[1:])) + + +if __name__ == "__main__": + new_to_orig_ids = create_name_mapping_from_tsv(ids_tsv) + restore_gff3_ids(new_to_orig_ids, input_gff3, f"{output_prefix}.restored.ids.gff3") diff --git a/modules/gallvp/custom/restoregffids/tests/main.nf.test b/modules/gallvp/custom/restoregffids/tests/main.nf.test new file mode 100644 index 0000000..2c248c9 --- /dev/null +++ b/modules/gallvp/custom/restoregffids/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process CUSTOM_RESTOREGFFIDS" + script "../main.nf" + process "CUSTOM_RESTOREGFFIDS" + + tag "modules" + tag "modules_gallvp" + tag "custom" + tag "custom/restoregffids" + + test("sarscov2-genome_gff3-success") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + ] + input[1] = Channel.of('Chr1\tMT192765.1').collectFile(name: 'id_map.tsv', newLine: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert path(process.out.restored_ids_gff3.get(0).get(1)).getText().contains("Chr1") }, + { assert !path(process.out.restored_ids_gff3.get(0).get(1)).getText().contains("MT192765.1") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + ] + input[1] = Channel.of('Chr1\tMT192765.1').collectFile(name: 'id_map.tsv', newLine: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.restored_ids_gff3 != null }, + { assert snapshot(process.out.versions).match("versions_stub") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/gallvp/custom/restoregffids/tests/main.nf.test.snap b/modules/gallvp/custom/restoregffids/tests/main.nf.test.snap new file mode 100644 index 0000000..ebe850a --- /dev/null +++ b/modules/gallvp/custom/restoregffids/tests/main.nf.test.snap @@ -0,0 +1,61 @@ +{ + "sarscov2-genome_gff3-success": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.restored.ids.gff3:md5,2c294938b9eb4e52d19e14725c1d92a9" + ] + ], + "1": [ + "versions.yml:md5,32d31c4f1da9a3d1be013fd163e5867e" + ], + "restored_ids_gff3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.restored.ids.gff3:md5,2c294938b9eb4e52d19e14725c1d92a9" + ] + ], + "versions": [ + "versions.yml:md5,32d31c4f1da9a3d1be013fd163e5867e" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2023-12-07T13:49:30.047425" + }, + "versions_stub": { + "content": [ + [ + "versions.yml:md5,32d31c4f1da9a3d1be013fd163e5867e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-10T15:26:11.66528" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,32d31c4f1da9a3d1be013fd163e5867e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2023-12-07T13:49:30.071175" + } +} \ No newline at end of file diff --git a/modules/gallvp/custom/shortenfastaids/environment.yml b/modules/gallvp/custom/shortenfastaids/environment.yml new file mode 100644 index 0000000..04ccfc9 --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - biopython==1.75 + - python==3.8.13 diff --git a/modules/gallvp/custom/shortenfastaids/main.nf b/modules/gallvp/custom/shortenfastaids/main.nf new file mode 100644 index 0000000..886a626 --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/main.nf @@ -0,0 +1,38 @@ +process CUSTOM_SHORTENFASTAIDS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/biopython:1.75': + 'biocontainers/biopython:1.75' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.short.ids.fasta") , emit: short_ids_fasta , optional: true + tuple val(meta), path("*.short.ids.tsv") , emit: short_ids_tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + template 'shorten_fasta_ids.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo \\ + 'IDs have acceptable length and character. No change required.' \\ + > ${meta.id}.short.ids.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | cut -d' ' -f2) + biopython: \$(pip list | grep "biopython" | cut -d' ' -f3) + END_VERSIONS + """ +} diff --git a/modules/gallvp/custom/shortenfastaids/meta.yml b/modules/gallvp/custom/shortenfastaids/meta.yml new file mode 100644 index 0000000..bb14b0a --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/meta.yml @@ -0,0 +1,66 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_shortenfastaids" +description: | + Shortens fasta IDs and produces a new fasta along with a TSV table + consisting of original (first column) and new IDs (second column). + This module is helpful when some tools like EDTA implicitly shorten + the IDs without producing the ID map, leading to downstream mismatch + in IDs across files. +keywords: + - genome + - fasta + - ID + - shorten +tools: + - "biopython": + description: | + Biopython is a set of freely available tools for biological computation written in Python by + an international team of developers. + homepage: "https://biopython.org" + documentation: "https://biopython.org/wiki/Documentation" + tool_dev_url: "https://github.com/biopython/biopython" + doi: "10.1093/bioinformatics/btp163" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Input fasta file + pattern: "*.{fsa,fa,fasta}" +output: + - short_ids_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.short.ids.fasta": + type: file + description: Fasta file with shortened ids if id change is required + pattern: "*.{fsa,fa,fasta}" + - short_ids_tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.short.ids.tsv": + type: file + description: | + A TSV file with original (first column) and new ids (second column) + if id change is required + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@GallVp" +maintainers: + - "@GallVp" diff --git a/modules/gallvp/custom/shortenfastaids/templates/shorten_fasta_ids.py b/modules/gallvp/custom/shortenfastaids/templates/shorten_fasta_ids.py new file mode 100755 index 0000000..9d9c6e1 --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/templates/shorten_fasta_ids.py @@ -0,0 +1,168 @@ +#!/usr/bin/env python3 + +import re +from importlib.metadata import version +from platform import python_version + +from Bio import SeqIO + +# The input fasta file path +fasta_file_path = "$fasta" +output_files_prefix = "$prefix" + + +def extract_fasta_ids_and_descriptions(fasta_file_path): + fasta_file_obj = SeqIO.parse(fasta_file_path, "fasta") + + ids = [] + for record in fasta_file_obj: + ids.append((record.id, record.description)) + return ids + + +def write_fasta_with_new_ids(fasta_file_path, id_mapping, file_prefix): + old_fasta_file_obj = SeqIO.parse(fasta_file_path, "fasta") + id_map = dict(id_mapping) + + replaced_records = [] + for record in old_fasta_file_obj: + old_id = record.id + + new_id = id_map[old_id] + record.id = new_id + record.description = "" + + replaced_records.append(record) + + SeqIO.write(replaced_records, f"{file_prefix}.short.ids.fasta", "fasta") + + +def do_id_need_to_change(id_and_description, silent=False): + id = id_and_description[0] + description = id_and_description[1] + if len(id) > 13: + if not silent: + print(f"{id} has length greater than 13") + return True + + if not re.match(r"^[a-zA-Z0-9_]+\$", id): + if not silent: + print(f"{id} does not match '^[a-zA-Z0-9_]+\$'") + return True + + if description != id and description != "": + if not silent: + print(f"{id} contains a comment: {description.replace(id, '')}") + return True + + if not silent: + print(f"{id} is acceptable") + return False + + +def do_ids_need_to_change(ids_and_descriptions, silent=False): + return any([do_id_need_to_change(id_and_description, silent) for id_and_description in ids_and_descriptions]) + + +def extract_common_patterns(ids): + pattern_counts = {} + for id in ids: + patterns = re.findall(r"[A-Za-z0_]{4,}", id) + for pattern in set(patterns): + pattern_counts[pattern] = pattern_counts.get(pattern, 0) + 1 + + common_patterns = [pattern for pattern, count in pattern_counts.items() if count >= 2] + + if len(common_patterns) < 1: + return {} + + return {pattern: pattern[:3] for pattern in common_patterns} + + +def shorten_ids(input_ids_and_descriptions, patterns_dict): + shortened_ids = [] + + for id_and_description in input_ids_and_descriptions: + id = id_and_description[0] + description = "" # Treat description as absent as it will be removed by write_fasta_with_new_ids + if not do_id_need_to_change((id, description), silent=True): + shortened_ids.append(id) + continue + + shortened_id = shorten_id_by_pattern_replacement(patterns_dict, id) + + if not do_id_need_to_change((shortened_id, description), silent=True): + shortened_ids.append(shortened_id) + continue + + shortened_id = f"Ctg{generate_hash(id)}" + + if not do_id_need_to_change((shortened_id, description), silent=True): + shortened_ids.append(shortened_id) + continue + + raise ValueError(f"Failed to shorten id: {id} ({shortened_id})") + + return shortened_ids + + +def shorten_id_by_pattern_replacement(patterns_dict, id): + if patterns_dict == {}: + return id + + shortened_id = id + matches_for_id = match_substrings(patterns_dict.keys(), shortened_id) + + for pattern in matches_for_id: + shortened_id = re.sub( + rf"({re.escape(pattern)})", + patterns_dict[pattern], + shortened_id, + ) + return shortened_id if shortened_id[len(shortened_id) - 1] != "_" else shortened_id[0 : (len(shortened_id) - 1)] + + +def match_substrings(substrings, target_string): + pattern = "|".join(map(re.escape, substrings)) + matches = re.findall(pattern, target_string) + return matches + + +def generate_hash(string): + import hashlib + + hash_object = hashlib.sha1(string.encode()) + full_hash = hash_object.hexdigest() + short_hash = full_hash[:10] + return short_hash + + +def fail_if_new_ids_not_valid(ids): + if len(ids) != len(set(ids)): + raise ValueError("Th new IDs are not unique") + + +if __name__ == "__main__": + input_ids_and_descriptions = extract_fasta_ids_and_descriptions(fasta_file_path) + input_ids = [x[0] for x in input_ids_and_descriptions] + + # Write versions + with open("versions.yml", "w") as f_versions: + f_versions.write('"${task.process}":\\n') + f_versions.write(f" python: {python_version()}\\n") + f_versions.write(f" biopython: {version('biopython')}\\n") + + if not do_ids_need_to_change(input_ids_and_descriptions): + print("IDs have acceptable length and character. No change required.") + with open(f"{output_files_prefix}.short.ids.tsv", "w") as f: + f.write("IDs have acceptable length and character. No change required.") + exit(0) + + new_ids = shorten_ids(input_ids_and_descriptions, extract_common_patterns(input_ids)) + fail_if_new_ids_not_valid(new_ids) + + with open(f"{output_files_prefix}.short.ids.tsv", "w") as f: + for input_id, new_id in zip(input_ids, new_ids): + f.write(f"{input_id}\\t{new_id}\\n") + + write_fasta_with_new_ids(fasta_file_path, zip(input_ids, new_ids), output_files_prefix) diff --git a/modules/gallvp/custom/shortenfastaids/tests/main.nf.test b/modules/gallvp/custom/shortenfastaids/tests/main.nf.test new file mode 100644 index 0000000..8eb2099 --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/tests/main.nf.test @@ -0,0 +1,123 @@ +nextflow_process { + + name "Test Process CUSTOM_SHORTENFASTAIDS" + script "../main.nf" + process "CUSTOM_SHORTENFASTAIDS" + + tag "modules" + tag "modules_gallvp" + tag "custom" + tag "custom/shortenfastaids" + + test("homo_sapiens-genome_fasta-no_change") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2-genome_fasta-pattern_change") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens-genome2_fasta-length_change") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("custom_fasta-comment_change") { + + when { + process { + """ + input[0] = Channel.of('>Chr1 This is a test comment', 'AGCTAGCT') + | collectFile(name: 'sample.fasta', newLine: true) + | map { file -> [ [ id:'test' ], file ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/gallvp/custom/shortenfastaids/tests/main.nf.test.snap b/modules/gallvp/custom/shortenfastaids/tests/main.nf.test.snap new file mode 100644 index 0000000..2506ebd --- /dev/null +++ b/modules/gallvp/custom/shortenfastaids/tests/main.nf.test.snap @@ -0,0 +1,227 @@ +{ + "custom_fasta-comment_change": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,c861b9d46a4d9bdba66953cff572fc5d" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,8762f2bffbdff75c2812bad72ba52bba" + ] + ], + "2": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ], + "short_ids_fasta": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,c861b9d46a4d9bdba66953cff572fc5d" + ] + ], + "short_ids_tsv": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,8762f2bffbdff75c2812bad72ba52bba" + ] + ], + "versions": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2023-12-07T13:33:05.523745" + }, + "stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,fcf920d9a7b57a1e3c29a9e88673330f" + ] + ], + "2": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ], + "short_ids_fasta": [ + + ], + "short_ids_tsv": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,fcf920d9a7b57a1e3c29a9e88673330f" + ] + ], + "versions": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T13:58:30.161542" + }, + "homo_sapiens-genome_fasta-no_change": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,642382addc4beba37088b1ebe09d38cf" + ] + ], + "2": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ], + "short_ids_fasta": [ + + ], + "short_ids_tsv": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,642382addc4beba37088b1ebe09d38cf" + ] + ], + "versions": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.1" + }, + "timestamp": "2024-06-02T20:54:17.945233" + }, + "homo_sapiens-genome2_fasta-length_change": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,1382acd98d4cd233a8062ef01b2aaa6d" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,99c0f2a529cb595b2d8530024ed2880e" + ] + ], + "2": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ], + "short_ids_fasta": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,1382acd98d4cd233a8062ef01b2aaa6d" + ] + ], + "short_ids_tsv": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,99c0f2a529cb595b2d8530024ed2880e" + ] + ], + "versions": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2023-12-07T13:33:01.924483" + }, + "sarscov2-genome_fasta-pattern_change": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,14d6f587b6d28889c5c0f985e78d602f" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,d7a2af88e8549586e5616bff6a88bd71" + ] + ], + "2": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ], + "short_ids_fasta": [ + [ + { + "id": "test" + }, + "test.short.ids.fasta:md5,14d6f587b6d28889c5c0f985e78d602f" + ] + ], + "short_ids_tsv": [ + [ + { + "id": "test" + }, + "test.short.ids.tsv:md5,d7a2af88e8549586e5616bff6a88bd71" + ] + ], + "versions": [ + "versions.yml:md5,e5704a53ebea373dac3a93ae800d48ba" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2023-12-07T13:32:58.12885" + } +} \ No newline at end of file diff --git a/modules/gallvp/tirlearner/main.nf b/modules/gallvp/tirlearner/main.nf index c253245..2e0809d 100644 --- a/modules/gallvp/tirlearner/main.nf +++ b/modules/gallvp/tirlearner/main.nf @@ -50,12 +50,11 @@ process TIRLEARNER { cat <<-END_VERSIONS > versions.yml "${task.process}": - TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //') + TIR-Learner: \$(TIR-Learner -v | sed -n 's|TIR-Learner \\(.*\\) by .*|\\1|p') END_VERSIONS """ stub: - def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" if ( "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ @@ -69,7 +68,7 @@ process TIRLEARNER { cat <<-END_VERSIONS > versions.yml "${task.process}": - TIR-Learner: \$(TIR-Learner -v | head -n 1 | sed 's/TIR-Learner //') + TIR-Learner: \$(TIR-Learner -v | sed -n 's|TIR-Learner \\(.*\\) by .*|\\1|p') END_VERSIONS """ } diff --git a/modules/gallvp/tirlearner/tests/main.nf.test.snap b/modules/gallvp/tirlearner/tests/main.nf.test.snap index dd1a6d0..e6b52a0 100644 --- a/modules/gallvp/tirlearner/tests/main.nf.test.snap +++ b/modules/gallvp/tirlearner/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "sarscov2-genome": { "content": [ [ - "versions.yml:md5,9db74013377c09d8452530315592acdf" + "versions.yml:md5,054eb77998e320f8b70cae832f7bff59" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:03:25.394783" + "timestamp": "2024-12-17T15:23:12.222704" }, "actinidia_chinensis-genome_1_fasta_gz-success": { "content": [ @@ -46,14 +46,14 @@ ] ], [ - "versions.yml:md5,9db74013377c09d8452530315592acdf" + "versions.yml:md5,054eb77998e320f8b70cae832f7bff59" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:21:08.136874" + "timestamp": "2024-12-17T15:22:50.978766" }, "stub": { "content": [ @@ -99,7 +99,7 @@ ] ], "5": [ - "versions.yml:md5,9db74013377c09d8452530315592acdf" + "versions.yml:md5,054eb77998e320f8b70cae832f7bff59" ], "fasta": [ [ @@ -142,14 +142,14 @@ ] ], "versions": [ - "versions.yml:md5,9db74013377c09d8452530315592acdf" + "versions.yml:md5,054eb77998e320f8b70cae832f7bff59" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T12:56:16.022839" + "timestamp": "2024-12-17T15:23:25.302007" } } \ No newline at end of file diff --git a/modules/local/sanitize/main.nf b/modules/local/sanitize/main.nf deleted file mode 100644 index c1519af..0000000 --- a/modules/local/sanitize/main.nf +++ /dev/null @@ -1,38 +0,0 @@ -// Rename FASTA headers (just makes everything easier later) - -process SANITIZE_HEADERS { - tag "$meta.id" - label 'process_single' - - // Eventually port fffx (pronounced f3x) to bioconda - // conda "${moduleDir}/environment.yml" - // container "docker.io/gallvp/edta-components:v0.1" - - container "${ workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' - ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' - : 'nf-core/ubuntu:20.04' }" - - input: - tuple val(meta), path(fasta) - - output: - tuple val(meta), path('*.sanitized.fasta'), emit: fasta - tuple val(meta), path('*.sanitized.translation_table.tsv'), emit: translation_table - eval('fffx --version'), topic: versions - - - when: - task.ext.when == null || task.ext.when - - script: - """ - fffx length-filter ${fasta} filtered.fa 1000 - fffx sanitize filtered.fa ${fasta.baseName}.sanitized - """ - - stub: - """ - touch ${fasta.baseName}.sanitized.fasta - touch ${fasta.baseName}.sanitized.translation_table.tsv - """ -} \ No newline at end of file diff --git a/tests/nf-test/small/main.nf.test b/tests/nf-test/small/main.nf.test index 43e207c..87b44cb 100644 --- a/tests/nf-test/small/main.nf.test +++ b/tests/nf-test/small/main.nf.test @@ -7,7 +7,7 @@ nextflow_pipeline { when { params { - genome = "https://raw.githubusercontent.com/jguhlin/EDTA/a2cd9a0777e4ac6e39545bacc3e752f94eb2f389/test/genome.fa" + genome = "https://raw.githubusercontent.com/oushujun/EDTA/4f0424b8a3ce2caccdd51b4021c61a536fa9ead9/test/genome.fa" outdir = "$outputDir" } } @@ -19,18 +19,9 @@ nextflow_pipeline { false, [ 'pipeline_info/*.{html,json,txt,yml}', - 'raw/ltr/*.LTR.intact.gff3', - 'raw/ltr/*.LTR.fa', - 'raw/tir/*.TIR.intact.fa', - 'raw/tir/*.TIR.intact.gff3', - 'raw/line/*.LINE.fa', - 'raw/line/*.RM2.fa', - 'raw/helitron/*.Helitron.intact.fa', - 'raw/helitron/*.Helitron.intact.anno.list', - 'raw/helitron/*.Helitron.intact.gff3', - 'raw/intact/*', - 'stg1/*.fasta', - 'final/*' + 'genome/*.intact.fa', + 'genome/*.intact.gff3', + 'genome/*.TElib.fa' ], null, ['**'] @@ -46,6 +37,9 @@ nextflow_pipeline { ['**'] ) + def te_lib_count = file("$outputDir/genome/genome.TElib.fa").readLines().findAll { it.startsWith('>') }.size() + def intact_lib_count = file("$outputDir/genome/genome.intact.fa").readLines().findAll { it.startsWith('>') }.size() + assertAll( { assert workflow.success}, { assert snapshot( @@ -53,9 +47,11 @@ nextflow_pipeline { 'successful tasks': workflow.trace.succeeded().size(), 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), 'stable paths': stable_path, - 'stable names': getRelativePath(stable_name, outputDir), + 'stable names': getRelativePath(stable_name, outputDir) ] - ).match() } + ).match() }, + { assert Math.abs(te_lib_count - 45) <= 5.0 }, + { assert Math.abs(intact_lib_count - 42) <= 5.0 } ) } diff --git a/tests/nf-test/small/main.nf.test.snap b/tests/nf-test/small/main.nf.test.snap index dccc812..06527a9 100644 --- a/tests/nf-test/small/main.nf.test.snap +++ b/tests/nf-test/small/main.nf.test.snap @@ -13,6 +13,10 @@ "COMBINE_INTACT_TES": { "perl": "v5.32.1" }, + "CUSTOM_SHORTENFASTAIDS": { + "python": "3.8.13", + "biopython": 1.75 + }, "FINAL_FILTER": { "perl": "v5.32.1", "repeatmasker": "4.1.7-p1" @@ -81,7 +85,7 @@ "repeatmodeler": "2.0.5" }, "TIRLEARNER": { - "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + "TIR-Learner": "v3.0.2" }, "TIR_LEARNER_POSTPROCESS": { "perl": "v5.32.1", @@ -94,40 +98,15 @@ } }, "stable paths": [ - "genome.Helitron.intact.bed:md5,a8b170a1ee8d36c7f8e3af5ba1e43cb6", - "genome.LTR.intact.anno.list:md5,51261f020350b448acdf89d8fb625448", - "genome.LTR.intact.fa:md5,ae2336f498897d1af4e8d3be28bb3f25", - "genome.TIR.intact.bed:md5,12406184046b11edc2ddadbc82765966" + "genome.short.ids.tsv:md5,642382addc4beba37088b1ebe09d38cf" ], "stable names": [ - "final", - "final/genome.TElib.fa", - "final/genome.intact.fa", - "final/genome.intact.gff3", - "pipeline_info", - "raw", - "raw/helitron", - "raw/helitron/genome.Helitron.intact.anno.list", - "raw/helitron/genome.Helitron.intact.bed", - "raw/helitron/genome.Helitron.intact.fa", - "raw/helitron/genome.Helitron.intact.gff3", - "raw/intact", - "raw/intact/genome.intact.fa", - "raw/intact/genome.intact.gff3", - "raw/line", - "raw/line/genome.RM2.fa", - "raw/ltr", - "raw/ltr/genome.LTR.fa", - "raw/ltr/genome.LTR.intact.anno.list", - "raw/ltr/genome.LTR.intact.fa", - "raw/ltr/genome.LTR.intact.gff3", - "raw/tir", - "raw/tir/genome.TIR.intact.bed", - "raw/tir/genome.TIR.intact.fa", - "raw/tir/genome.TIR.intact.gff3", - "stg1", - "stg1/genome.fasta", - "stg1/genome.intact.fasta" + "genome", + "genome/genome.TElib.fa", + "genome/genome.intact.fa", + "genome/genome.intact.gff3", + "genome/genome.short.ids.tsv", + "pipeline_info" ] } ], @@ -135,6 +114,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T14:02:22.882318" + "timestamp": "2024-12-17T22:28:58.604502" } } \ No newline at end of file diff --git a/tests/nf-test/tiny/main.nf.test b/tests/nf-test/tiny/main.nf.test index 0a92bd5..2b90162 100644 --- a/tests/nf-test/tiny/main.nf.test +++ b/tests/nf-test/tiny/main.nf.test @@ -13,7 +13,8 @@ nextflow_pipeline { } then { - def stable_path = getAllFilesFromDir(params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**']) + def stable_path = getAllFilesFromDir ( params.outdir, false, ['pipeline_info/*.{html,json,txt,yml}'], null, ['**'] ) + def stable_name = getAllFilesFromDir ( params.outdir, true, [ 'pipeline_info/*.{html,json,txt,yml}' ], null, ['**'] ) assertAll( { assert workflow.success}, @@ -21,7 +22,8 @@ nextflow_pipeline { [ 'successful tasks': workflow.trace.succeeded().size(), 'versions': removeNextflowVersion("$outputDir/pipeline_info/software_versions.yml"), - 'stable paths': stable_path + 'stable paths': stable_path, + 'stable names': getRelativePath(stable_name, outputDir) ] ).match() } ) diff --git a/tests/nf-test/tiny/main.nf.test.snap b/tests/nf-test/tiny/main.nf.test.snap index 896e0b8..40e5592 100644 --- a/tests/nf-test/tiny/main.nf.test.snap +++ b/tests/nf-test/tiny/main.nf.test.snap @@ -10,6 +10,10 @@ "CAT_CAT": { "pigz": "2.3.4" }, + "CUSTOM_SHORTENFASTAIDS": { + "python": "3.8.13", + "biopython": 1.75 + }, "FORMAT_HELITRONSCANNER_OUT": { "perl": "v5.32.1" }, @@ -46,14 +50,19 @@ "LTR_retriever": "v2.9.9" }, "TIRLEARNER": { - "TIR-Learner": "v3.0.2 by Tianyu (Sky) Lu (tlu83@wisc.edu) published under GPLv3" + "TIR-Learner": "v3.0.2" }, "Workflow": { "oushujun/EDTA": "v0.1.0dev" } }, "stable paths": [ - + "genome.short.ids.tsv:md5,d7a2af88e8549586e5616bff6a88bd71" + ], + "stable names": [ + "genome", + "genome/genome.short.ids.tsv", + "pipeline_info" ] } ], @@ -61,6 +70,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2024-12-13T09:54:27.064885" + "timestamp": "2024-12-17T17:06:09.728972" } } \ No newline at end of file diff --git a/workflows/edta.nf b/workflows/edta.nf index 1f13998..1d9bb26 100644 --- a/workflows/edta.nf +++ b/workflows/edta.nf @@ -1,4 +1,6 @@ -include { SANITIZE_HEADERS } from '../modules/local/sanitize/main' +include { GUNZIP } from '../modules/gallvp/gunzip/main' +include { CUSTOM_SHORTENFASTAIDS } from '../modules/gallvp/custom/shortenfastaids/main' +include { CUSTOM_RESTOREGFFIDS } from '../modules/gallvp/custom/restoregffids/main' include { LTRHARVEST } from '../modules/nf-core/ltrharvest/main' include { LTRFINDER } from '../modules/nf-core/ltrfinder/main' @@ -36,18 +38,49 @@ workflow EDTA { ch_versions = Channel.empty() - ch_genome = Channel.fromPath(params.genome) + ch_genome_branch = Channel.fromPath(params.genome) | map { genome -> def meta = [:] meta.id = idFromFileName ( genome.baseName ) [ meta, genome ] } + | branch { _meta, archive -> + gz: "$archive".endsWith('.gz') + rest: ! "$archive".endsWith('.gz') + } + + // MODULE: GUNZIP + GUNZIP ( ch_genome_branch.gz ) - // MODULE: SANITIZE_HEADERS - SANITIZE_HEADERS ( ch_genome ) + ch_genome = GUNZIP.out.gunzip.mix(ch_genome_branch.rest) + ch_versions = ch_versions.mix(GUNZIP.out.versions.first()) - ch_sanitized_fasta = SANITIZE_HEADERS.out.fasta + // MODULE: CUSTOM_SHORTENFASTAIDS + CUSTOM_SHORTENFASTAIDS ( ch_genome ) + + ch_short_ids_tsv = CUSTOM_SHORTENFASTAIDS.out.short_ids_tsv + ch_versions = ch_versions.mix(CUSTOM_SHORTENFASTAIDS.out.versions.first()) + + + ch_shortenfastaids_branch = ch_short_ids_tsv + | branch { _meta, tsv -> + change: ! tsv.text.contains('IDs have acceptable length and character') + nochange: tsv.text.contains('IDs have acceptable length and character') + } + + ch_sanitized_fasta = ch_shortenfastaids_branch.nochange + | join( + ch_genome + ) + | map { meta, _tsv, fasta -> [ meta + [ changed_ids: false ], fasta ] } + | mix( + ch_shortenfastaids_branch.change + | join( + CUSTOM_SHORTENFASTAIDS.out.short_ids_fasta + ) + | map { meta, _tsv, fasta -> [ meta + [ changed_ids: true ], fasta ] } + ) // MODULE: LTRHARVEST LTRHARVEST ( ch_sanitized_fasta ) @@ -344,8 +377,23 @@ workflow EDTA { ch_final_filter_inputs.intact_gff, ) + ch_intact_gff = FINAL_FILTER.out.intact_gff ch_versions = ch_versions.mix(FINAL_FILTER.out.versions.first()) + // MODULE: CUSTOM_RESTOREGFFIDS + ch_gff_tsv_branch = ch_intact_gff.join(ch_short_ids_tsv) + | branch { meta, _gff, _tsv -> + change: meta.changed_ids + nochange: ! meta.changed_ids + } + + CUSTOM_RESTOREGFFIDS ( + ch_gff_tsv_branch.change.map { meta, gff, _tsv -> [ meta, gff ] }, + ch_gff_tsv_branch.change.map { _meta, _gff, tsv -> tsv } + ) + + ch_versions = ch_versions.mix(CUSTOM_RESTOREGFFIDS.out.versions.first()) + // Function: Save versions ch_versions = ch_versions | unique From 438b78f94eb2fe3e4d67d6656a293292e908f925 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Wed, 18 Dec 2024 11:11:09 +1300 Subject: [PATCH 46/49] Added parameter validation by nf-schema --- .github/PULL_REQUEST_TEMPLATE.md | 12 +- .github/workflows/ci.yml | 2 +- .gitignore | 1 + cleanNXF.sh | 3 + conf/base.config | 49 ++ conf/modules.config | 30 +- conf/test.config | 4 +- conf/test_full.config | 11 + main.nf | 25 +- modules.json | 19 + modules/local/utils/main.nf | 65 --- nextflow.config | 255 ++++++++--- nextflow_schema.json | 93 ++++ .../local/utils_nfcore_edta_pipeline/main.nf | 114 +++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 ++++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 20 + .../tests/main.workflow.nf.test | 113 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 419 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 126 ++++++ .../tests/main.function.nf.test.snap | 136 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 19 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfschema_plugin/main.nf | 46 ++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 +++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 96 ++++ workflows/edta.nf | 14 +- 35 files changed, 1948 insertions(+), 177 deletions(-) create mode 100644 conf/base.config create mode 100644 conf/test_full.config delete mode 100644 modules/local/utils/main.nf create mode 100644 nextflow_schema.json create mode 100644 subworkflows/local/utils_nfcore_edta_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 7919df0..eb3ed74 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -9,12 +9,6 @@ These are the most common things requested on pull requests (PRs). ## PR checklist -For Nextflow implementation, - -- [ ] `conda` and `container` directives are included for each process -- [ ] Docker container + singularity container (optional) are included for each process -- [ ] Flow `meta.id` with each data channel -- [ ] Use nf-core resource labels such as `process_high` -- [ ] Used nf-core module -- [ ] Use `versions.yml` or versions topic -- [ ] No process in the `main.nf`. We can have a process in a sub-workflow file +- [ ] This comment contains a description of changes (with reason). +- [ ] If you've fixed a bug or added code that should be tested, add tests! +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d53140c..3a33d22 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,7 +46,7 @@ jobs: fail-fast: false matrix: NXF_VER: - - "24.04.2" + - "24.10.3" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: [conda, docker, singularity] diff --git a/.gitignore b/.gitignore index f636970..3a9b5c2 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ work/ .nextflow/* results/ .nf-test* +null/ diff --git a/cleanNXF.sh b/cleanNXF.sh index 81b8d85..9752c09 100755 --- a/cleanNXF.sh +++ b/cleanNXF.sh @@ -13,3 +13,6 @@ echo "Cleaned work..." rm -f .nf-test.log rm -rf .nf-test echo "Cleaned nf-test..." + +rm -rf null +echo "Cleaned null..." diff --git a/conf/base.config b/conf/base.config new file mode 100644 index 0000000..643430d --- /dev/null +++ b/conf/base.config @@ -0,0 +1,49 @@ +process { + + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + maxRetries = 1 + maxErrors = '-1' + + // Process-specific resource requirements + // NOTE - Please try and re-use the labels below as much as possible. + // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. + // If possible, it would be nice to keep the same label naming convention when + // adding in your local modules too. + withLabel:process_single { + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } + } + withLabel:process_low { + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } + } + withLabel:process_medium { + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } + } + withLabel:process_high { + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } + } + withLabel:process_long { + time = { 20.h * task.attempt } + } + withLabel:process_high_memory { + memory = { 200.GB * task.attempt } + } + withLabel:error_ignore { + errorStrategy = 'ignore' + } + withLabel:error_retry { + errorStrategy = 'retry' + maxRetries = 2 + } +} \ No newline at end of file diff --git a/conf/modules.config b/conf/modules.config index 0bce9d9..47b5804 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,6 +1,6 @@ process { - withName: 'EDTA:CUSTOM_SHORTENFASTAIDS' { + withName: 'OUSHUJUN_EDTA:EDTA:CUSTOM_SHORTENFASTAIDS' { publishDir = [ path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, @@ -8,60 +8,60 @@ process { ] } - withName: 'EDTA:LTRHARVEST' { + withName: 'OUSHUJUN_EDTA:EDTA:LTRHARVEST' { ext.args = '-size 1000000 -time 300' ext.prefix = { "${meta.id}_ltrharvest" } } - withName: 'EDTA:LTRFINDER' { + withName: 'OUSHUJUN_EDTA:EDTA:LTRFINDER' { ext.args = '-harvest_out -size 1000000 -time 300' } - withName: 'EDTA:CAT_CAT' { + withName: 'OUSHUJUN_EDTA:EDTA:CAT_CAT' { ext.prefix = { "${meta.id}_ltrharvest_ltrfinder.tabout" } } - withName: 'EDTA:ANNOSINE' { + withName: 'OUSHUJUN_EDTA:EDTA:ANNOSINE' { ext.prefix = { "${meta.id}.annosine" } ext.args = params.annosine_ext_args ?: '-a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1' } - withName: 'EDTA:REPEATMODELER_REPEATMODELER' { + withName: 'OUSHUJUN_EDTA:EDTA:REPEATMODELER_REPEATMODELER' { ext.args = '-engine ncbi' } - withName: 'EDTA:TIRLEARNER' { + withName: 'OUSHUJUN_EDTA:EDTA:TIRLEARNER' { ext.prefix = { "${meta.id}.tirlearner" } } - withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { + withName: 'OUSHUJUN_EDTA:EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW' { ext.args = '-pure_helitron' } - withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { + withName: 'OUSHUJUN_EDTA:EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_HEAD_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { + withName: 'OUSHUJUN_EDTA:EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_SCAN_TAIL_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '--rc' } - withName: 'EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { + withName: 'OUSHUJUN_EDTA:EDTA:FASTA_HELITRONSCANNER_SCAN_DRAW:HELITRONSCANNER_DRAW_RC' { ext.prefix = { "${meta.id}.rc" } ext.args = '-pure_helitron' } - withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT' { + withName: 'OUSHUJUN_EDTA:EDTA:FORMAT_HELITRONSCANNER_OUT' { ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extout 0' } - withName: 'EDTA:FORMAT_HELITRONSCANNER_OUT_EXT' { + withName: 'OUSHUJUN_EDTA:EDTA:FORMAT_HELITRONSCANNER_OUT_EXT' { ext.args = '-sitefilter 1 -minscore 12 -keepshorter 1 -extlen 30 -extout 1' } - withName: 'EDTA:FINAL_FILTER' { + withName: 'OUSHUJUN_EDTA:EDTA:FINAL_FILTER' { publishDir = [ path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, @@ -76,7 +76,7 @@ process { ] } - withName: 'EDTA:CUSTOM_RESTOREGFFIDS' { + withName: 'OUSHUJUN_EDTA:EDTA:CUSTOM_RESTOREGFFIDS' { publishDir = [ path: { "${params.outdir}/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/conf/test.config b/conf/test.config index 6d0509d..ce76591 100644 --- a/conf/test.config +++ b/conf/test.config @@ -4,8 +4,8 @@ params { process { resourceLimits = [ - cpus: 10, - memory: '32.GB', + cpus: 4, + memory: '15.GB', time: '1.h' ] } diff --git a/conf/test_full.config b/conf/test_full.config new file mode 100644 index 0000000..6d0509d --- /dev/null +++ b/conf/test_full.config @@ -0,0 +1,11 @@ +params { + genome = 'https://raw.githubusercontent.com/oushujun/EDTA/4f0424b8a3ce2caccdd51b4021c61a536fa9ead9/test/genome.fa' +} + +process { + resourceLimits = [ + cpus: 10, + memory: '32.GB', + time: '1.h' + ] +} diff --git a/main.nf b/main.nf index a50616d..3a9c8ce 100755 --- a/main.nf +++ b/main.nf @@ -2,8 +2,27 @@ nextflow.enable.dsl = 2 -include { EDTA } from './workflows/edta.nf' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_edta_pipeline' +include { EDTA } from './workflows/edta.nf' -workflow { - EDTA() +workflow OUSHUJUN_EDTA { + + take: + ch_genome + + main: + EDTA ( ch_genome ) } + +workflow { + + main: + PIPELINE_INITIALISATION ( + params.version, + args, + params.outdir, + params.genome + ) + + OUSHUJUN_EDTA ( PIPELINE_INITIALISATION.out.genome ) +} \ No newline at end of file diff --git a/modules.json b/modules.json index b012c3e..772b7c4 100644 --- a/modules.json +++ b/modules.json @@ -91,6 +91,25 @@ "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "installed_by": ["subworkflows"] + }, + "utils_nfschema_plugin": { + "branch": "master", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/utils/main.nf b/modules/local/utils/main.nf deleted file mode 100644 index dea2b26..0000000 --- a/modules/local/utils/main.nf +++ /dev/null @@ -1,65 +0,0 @@ -// -// Generate workflow version string -// -def getWorkflowVersion() { - def version_string = "" as String - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string -} - -// -// Get software versions for pipeline -// -def processVersionsFromYAML(yaml_file) { - def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } - return yaml.dumpAsMap(versions).trim() -} - -// -// Get workflow version for pipeline -// -def workflowVersionToYAML() { - return """ - Workflow: - ${workflow.manifest.name}: ${getWorkflowVersion()} - Nextflow: ${workflow.nextflow.version} - """.stripIndent().trim() -} - -// -// Get channel of software versions used in pipeline in YAML format -// -def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) -} - -// -// Gen a working sample ID from a file name -// -def idFromFileName(fileName) { - - def trial = ( fileName - ).replaceFirst( - /\.f(ast)?q$/, '' - ).replaceFirst( - /\.f(asta|sa|a|as|aa|na)?$/, '' - ).replaceFirst( - /\.gff(3)?$/, '' - ).replaceFirst( - /\.gz$/, '' - ) - - if ( trial == fileName ) { return fileName } - - return idFromFileName ( trial ) -} diff --git a/nextflow.config b/nextflow.config index 25a0b75..c9c7aa1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,111 +1,220 @@ +// Global default params, used in configs params { - genome = 'genomes/*' - species = 'others' - outdir = 'results' + // Input/output options + genome = null + species = 'others' + outdir = null - annosine_ext_args = null + // CLI arguments for tools + annosine_ext_args = null - publish_dir_mode = 'copy' -} - -process { - - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } - - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' - - withLabel:process_single { - cpus = { 1 } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } - } - withLabel:process_low { - cpus = { 2 * task.attempt } - memory = { 12.GB * task.attempt } - time = { 4.h * task.attempt } - } - withLabel:process_medium { - cpus = { 6 * task.attempt } - memory = { 36.GB * task.attempt } - time = { 8.h * task.attempt } - } - withLabel:process_high { - cpus = { 12 * task.attempt } - memory = { 72.GB * task.attempt } - time = { 16.h * task.attempt } - } - withLabel:process_long { - time = { 20.h * task.attempt } - } - withLabel:process_high_memory { - memory = { 200.GB * task.attempt } - } - withLabel:error_ignore { - errorStrategy = 'ignore' - } - withLabel:error_retry { - errorStrategy = 'retry' - maxRetries = 2 - } + // Boilerplate options + version = false + publish_dir_mode = 'copy' } // Max resources process { resourceLimits = [ - cpus: 12, + cpus: 16, memory: '72.GB', - time: '7.days' + time: '7.day' ] } +// Load base.config by default for all pipelines +includeConfig 'conf/base.config' + profiles { - singularity { - singularity.enabled = true - singularity.autoMounts = true - } - apptainer { - apptainer.enabled = true - apptainer.autoMounts = true + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda'] + apptainer.enabled = false } mamba { conda.enabled = true conda.useMamba = true - } - podman { - podman.enabled = true - podman.userEmulation = true - podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always" + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' + } + arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } - test { includeConfig './conf/test.config' } + singularity { + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + } + podman { + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + } + shifter { + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + } + charliecloud { + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + gitpod { + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB + } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config' } } +apptainer.registry = 'quay.io' docker.registry = 'quay.io' podman.registry = 'quay.io' singularity.registry = 'quay.io' -apptainer.registry = 'quay.io' +charliecloud.registry = 'quay.io' -// Increase time available to build Conda environment -conda { - createTimeout = "120 min" +env { + PYTHONNOUSERSITE = 1 + R_PROFILE_USER = "/.Rprofile" + R_ENVIRON_USER = "/.Renviron" + JULIA_DEPOT_PATH = "/usr/local/share/julia" +} + +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" + +nextflow.enable.configProcessNamesValidation = false + +def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') +timeline { + enabled = true + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" +} +report { + enabled = true + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" +} +trace { + enabled = true + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" +} +dag { + enabled = true + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { name = 'oushujun/EDTA' - description = 'Extensive de-novo TE Annotator on Nextflow' - author = 'Shujun Ou, Usman Rashid & Joseph Guhlin' - version = '0.1.0dev' - nextflowVersion = '!>=23.04.0' + description = 'Extensive de-novo TE Annotator' + version = '3.0.0dev' + nextflowVersion = '!>=24.10.3' + contributors = [ + [ + name : 'Shujun Ou', + affiliation : 'Ohio State University', + github : 'https://github.com/oushujun', + contribution : 'author', + orcid : 'https://orcid.org/0000-0001-5938-7180' + ], + [ + name : 'Usman Rashid', + affiliation : 'Plant & Food Research', + github : 'https://github.com/GallVp', + contribution : 'contributor', + orcid : 'https://orcid.org/0000-0002-1109-5493' + ], + [ + name : 'Joseph Guhlin', + affiliation : 'Dunedin, New Zealand', + github : 'https://github.com/jguhlin', + contribution : 'contributor', + orcid : 'https://orcid.org/0000-0003-3264-7178' + ] + ] +} + +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --genome --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + + } } +// Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json new file mode 100644 index 0000000..825a9fb --- /dev/null +++ b/nextflow_schema.json @@ -0,0 +1,93 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/EDTA/master/nextflow_schema.json", + "title": "EDTA pipeline parameters", + "description": "Extensive de-novo TE Annotator", + "type": "object", + "$defs": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["genome", "outdir"], + "properties": { + "genome": { + "type": "string", + "fa_icon": "fas fa-dna", + "description": "Path to a genome Fasta file or to a text file containing paths to Fasta files", + "pattern": "^\\S+\\.f(a|asta|as|sa|na)(\\.gz)?$|^\\S+\\.txt$", + "format": "file-path" + }, + "species": { + "type": "string", + "default": "others", + "fa_icon": "fas fa-otter", + "description": "Specify the species for identification of TIR candidates", + "enum": ["Rice", "Maize", "others"] + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + } + } + }, + "cli_arguments_for_tools": { + "title": "CLI arguments for tools", + "type": "object", + "description": "Arguments to pass to tools", + "default": "", + "properties": { + "annosine_ext_args": { + "type": "string", + "fa_icon": "fas fa-terminal", + "description": "Arguments for AnnoSINE" + } + }, + "fa_icon": "fas fa-wrench" + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "fa_icon": "fas fa-copy", + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_output_options" + }, + { + "$ref": "#/$defs/cli_arguments_for_tools" + }, + { + "$ref": "#/$defs/generic_options" + } + ] +} diff --git a/subworkflows/local/utils_nfcore_edta_pipeline/main.nf b/subworkflows/local/utils_nfcore_edta_pipeline/main.nf new file mode 100644 index 0000000..77e5a66 --- /dev/null +++ b/subworkflows/local/utils_nfcore_edta_pipeline/main.nf @@ -0,0 +1,114 @@ +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + genome // string: Path to a genome fasta or a text file with a list of fasta files + + main: + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + UTILS_NFSCHEMA_PLUGIN ( + workflow, + true, // validate params + null + ) + + // + // Create input channels + // + ch_genome = genome.find(/^\S+\.f(a|asta|as|sa|na)(\.gz)?$/) + ? ( + // Fasta + Channel.fromPath(genome) + | map { fasta -> + def fa_file = file(fasta, checkIfExists: true) + + def meta = [:] + meta.id = idFromFileName ( fa_file.baseName ) + + [ meta, fa_file ] + } + ) + : ( + // Text file + Channel.fromPath(genome) + | map { text -> + def file_list = file(text, checkIfExists: true).readLines() + + if ( file_list == [] ) { + error "File list provided by --genome is empty" + } + + file_list + .collect { fasta -> + def fa_file = file(fasta, checkIfExists: true) + + def meta = [:] + meta.id = idFromFileName ( fa_file.baseName ) + + [ meta, fa_file ] + } + } + | flatten + | buffer ( size: 2 ) + ) + | groupTuple + | view + | map { meta, fastas -> validateFastaMetadata ( meta, fastas ) } + + emit: + genome = ch_genome +} + +// +// Additional validation +// +def idFromFileName(fileName) { + + def trial = ( fileName + ).replaceFirst( + /\.f(ast)?q$/, '' + ).replaceFirst( + /\.f(asta|sa|a|as|aa|na)?$/, '' + ).replaceFirst( + /\.gff(3)?$/, '' + ).replaceFirst( + /\.gz$/, '' + ) + + if ( trial == fileName ) { return fileName } + + return idFromFileName ( trial ) +} + +def validateFastaMetadata(meta, fastas) { + + if ( fastas.size() > 1 ) { + error "Multiple Fasta files have the same ID '${meta.id}'. Make sure all the files are unique and change file names to avoid this conflict!" + } + + [ meta, fastas.first() ] +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 0000000..d6e593e --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW DEFINITION +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + def parser = new org.yaml.snakeyaml.Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } + catch (NullPointerException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.debug(e) + log.warn("Could not verify conda channel configuration.") + return null + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } + + if (channels_missing | channel_priority_violation) { + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 0000000..e5c3a0a --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 0000000..68718e4 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 0000000..e3f0baf --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,20 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" + }, + "Test Function checkCondaChannels": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 0000000..02dbf09 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,113 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } + } + } + + test("Should dump params") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = 'results' + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = null + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 0000000..a09572e --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 0000000..f847611 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 0000000..bfd2587 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,419 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW DEFINITION +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow UTILS_NFCORE_PIPELINE { + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + def valid_config = true as Boolean + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) + } + if (nextflow_cli_args[0]) { + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) + } +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "