From 9f230645f538df7086c856795196c3d446321007 Mon Sep 17 00:00:00 2001 From: luisas Date: Fri, 13 Dec 2024 12:40:19 +0100 Subject: [PATCH] fix linting --- modules.json | 145 +++------- modules/nf-core/clustalo/align/main.nf | 2 +- .../nf-core/foldmason/easymsa/environment.yml | 4 +- .../foldmason/easymsa/foldmason-easymsa.diff | 6 +- modules/nf-core/foldmason/easymsa/main.nf | 7 +- .../foldmason/easymsa/tests/main.nf.test.snap | 32 +-- modules/nf-core/mafft/environment.yml | 6 - modules/nf-core/mafft/main.nf | 75 ------ modules/nf-core/mafft/meta.yml | 108 -------- modules/nf-core/mafft/tests/main.nf.test | 248 ----------------- modules/nf-core/mafft/tests/main.nf.test.snap | 250 ------------------ modules/nf-core/mafft/tests/tags.yml | 2 - subworkflows/local/preprocess.nf | 1 + subworkflows/local/visualization.nf | 2 + 14 files changed, 64 insertions(+), 824 deletions(-) delete mode 100644 modules/nf-core/mafft/environment.yml delete mode 100644 modules/nf-core/mafft/main.nf delete mode 100644 modules/nf-core/mafft/meta.yml delete mode 100644 modules/nf-core/mafft/tests/main.nf.test delete mode 100644 modules/nf-core/mafft/tests/main.nf.test.snap delete mode 100644 modules/nf-core/mafft/tests/tags.yml diff --git a/modules.json b/modules.json index 7a9db7e2..0dd59818 100644 --- a/modules.json +++ b/modules.json @@ -7,224 +7,157 @@ "nf-core": { "clustalo/align": { "branch": "master", - "git_sha": "2a8530b890878747f5063a894bad9fb2abd5c071", - "installed_by": [ - "modules" - ] + "git_sha": "7b32b09fe7787c0fc6924e7b6f223a0b1daf0d2f", + "installed_by": ["modules"] }, "clustalo/guidetree": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/concat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/join": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/csvtk/join/csvtk-join.diff" }, "famsa/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "famsa/guidetree": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastavalidator": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "foldmason/createdb": { "branch": "master", "git_sha": "0270c0fbbbb09456d7823605e4285c4a2c5bbf40", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "foldmason/easymsa": { "branch": "master", - "git_sha": "8541ec46706d6610b032748fa51acf4b3094ced8", - "installed_by": [ - "modules" - ], + "git_sha": "0270c0fbbbb09456d7823605e4285c4a2c5bbf40", + "installed_by": ["modules"], "patch": "modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff" }, "foldmason/msa2lddtreport": { "branch": "master", "git_sha": "d3555a4a33ae94269b65f79f7066ac2fcb836005", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kalign/align": { "branch": "master", "git_sha": "cadb9bbfe56001ac421e0ee87808b0ccc754593a", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/kalign/align/kalign-align.diff" }, "learnmsa/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] - }, - "mafft": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mafft/align": { "branch": "master", "git_sha": "868cb0d7fc4862991fb7c2b4cd7289806cd53f81", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mafft/guidetree": { "branch": "master", "git_sha": "968b494e20f439a9ed3d23c89274e6a4a625eb92", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "magus/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mtmalign/align": { "branch": "master", "git_sha": "4eecd9a0c06fa508ae314c06ac952c161c019679", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "muscle5/super5": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pigz/compress": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pigz/uncompress": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/align": { "branch": "master", "git_sha": "66b22564bc1bc0db7292f2073cdef954ead773e7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/alncompare": { "branch": "master", "git_sha": "ffa000ab3c33df25a165b5f9a039c4cbb665a77b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/consensus": { "branch": "master", "git_sha": "023e51187884ea6cc7290767486f551565f1b77a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/extractfrompdb": { "branch": "master", "git_sha": "1f94c91de2b9e9c6b42fca53e823cada9a8b8465", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/tcoffee/extractfrompdb/tcoffee-extractfrompdb.diff" }, "tcoffee/irmsd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/regressive": { "branch": "master", "git_sha": "66b22564bc1bc0db7292f2073cdef954ead773e7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/seqreformat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/tcs": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upp/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -233,26 +166,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "1b89f75f1aa2021ec3360d0deccd0f6e97240551", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/modules/nf-core/clustalo/align/main.nf b/modules/nf-core/clustalo/align/main.nf index e55ca172..c220afd7 100644 --- a/modules/nf-core/clustalo/align/main.nf +++ b/modules/nf-core/clustalo/align/main.nf @@ -31,7 +31,7 @@ process CLUSTALO_ALIGN { def fhmm_batch = hmm_batch ? "--hmm-batch=${hmm_batch}" : "" def fprofile1 = profile1 ? "--profile1=${profile1}" : "" def fprofile2 = profile2 ? "--profile2=${profile2}" : "" - def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln" + def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "-o ${prefix}.aln" // using >() is necessary to preserve the return value, // so nextflow knows to display an error when it failed // the --force -o is necessary, as clustalo expands the commandline input, diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml index 64a5b367..fa2909a9 100644 --- a/modules/nf-core/foldmason/easymsa/environment.yml +++ b/modules/nf-core/foldmason/easymsa/environment.yml @@ -1,8 +1,6 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::foldmason=1.763a428 + - bioconda::foldmason=2.7bd21ed - conda-forge::pigz=2.8 diff --git a/modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff b/modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff index eed347f6..b2f98159 100644 --- a/modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff +++ b/modules/nf-core/foldmason/easymsa/foldmason-easymsa.diff @@ -2,7 +2,7 @@ Changes in module 'nf-core/foldmason/easymsa' Changes in 'foldmason/easymsa/main.nf': --- modules/nf-core/foldmason/easymsa/main.nf +++ modules/nf-core/foldmason/easymsa/main.nf -@@ -12,7 +12,7 @@ +@@ -15,7 +15,7 @@ output: tuple val(meta), path("${prefix}_3di.fa${compress ? '.gz' : ''}"), emit: msa_3di @@ -11,7 +11,7 @@ Changes in 'foldmason/easymsa/main.nf': path "versions.yml" , emit: versions when: -@@ -33,7 +33,7 @@ +@@ -36,7 +36,7 @@ if ${compress}; then pigz -p ${task.cpus} ${prefix}_3di.fa @@ -20,7 +20,7 @@ Changes in 'foldmason/easymsa/main.nf': fi cat <<-END_VERSIONS > versions.yml -@@ -48,7 +48,7 @@ +@@ -51,7 +51,7 @@ prefix = task.ext.prefix ?: "${meta.id}" """ echo "" ${compress ? '| gzip' : ''} > ${prefix}_3di.fa${compress ? '.gz' : ''} diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf index b3357364..fbaf6487 100644 --- a/modules/nf-core/foldmason/easymsa/main.nf +++ b/modules/nf-core/foldmason/easymsa/main.nf @@ -3,7 +3,10 @@ process FOLDMASON_EASYMSA { label 'process_medium' conda "${moduleDir}/environment.yml" - container "community.wave.seqera.io/library/foldmason_pigz:54849036d93c89ed" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03': + 'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }" + input: tuple val(meta) , path(pdbs) @@ -31,8 +34,6 @@ process FOLDMASON_EASYMSA { $args \\ --threads $task.cpus - mv ${prefix}_aa.fa ${prefix}.fa - if ${compress}; then pigz -p ${task.cpus} ${prefix}_3di.fa pigz -p ${task.cpus} ${prefix}.fa diff --git a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap index 384d2021..4951f29b 100644 --- a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap +++ b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:56:12.836231763" + "timestamp": "2024-12-09T15:22:29.135105042" }, "Test on seatoxin dataset - uncompressed": { "content": [ @@ -68,7 +68,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -87,7 +87,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -95,7 +95,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:55:41.89060384" + "timestamp": "2024-12-09T15:21:46.797852094" }, "Test on seatoxin dataset - compressed": { "content": [ @@ -117,7 +117,7 @@ ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ @@ -136,7 +136,7 @@ ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -144,7 +144,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:55:52.135344443" + "timestamp": "2024-12-09T15:21:58.958099076" }, "Test on seatoxin dataset - guide_tree": { "content": [ @@ -154,7 +154,7 @@ { "id": "test" }, - "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4" + "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" ] ], "1": [ @@ -162,18 +162,18 @@ { "id": "test" }, - "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae" + "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" ] ], "2": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ], "msa_3di": [ [ { "id": "test" }, - "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4" + "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" ] ], "msa_aa": [ @@ -181,11 +181,11 @@ { "id": "test" }, - "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae" + "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" ] ], "versions": [ - "versions.yml:md5,da4694171d1b0bb9559f7049334126ed" + "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6" ] } ], @@ -193,6 +193,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-04T10:56:02.473496089" + "timestamp": "2024-12-09T15:22:11.0778334" } } \ No newline at end of file diff --git a/modules/nf-core/mafft/environment.yml b/modules/nf-core/mafft/environment.yml deleted file mode 100644 index 97a13e68..00000000 --- a/modules/nf-core/mafft/environment.yml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::mafft=7.520 - - conda-forge::pigz=2.8 diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf deleted file mode 100644 index f09a0c96..00000000 --- a/modules/nf-core/mafft/main.nf +++ /dev/null @@ -1,75 +0,0 @@ -process MAFFT { - 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/mulled-v2-12eba4a074f913c639117640936668f5a6a01da6:425707898cf4f85051b77848be253b88f1d2298a-0': - 'biocontainers/mulled-v2-12eba4a074f913c639117640936668f5a6a01da6:425707898cf4f85051b77848be253b88f1d2298a-0' }" - - input: - tuple val(meta) , path(fasta) - tuple val(meta2), path(add) - tuple val(meta3), path(addfragments) - tuple val(meta4), path(addfull) - tuple val(meta5), path(addprofile) - tuple val(meta6), path(addlong) - val(compress) - - output: - tuple val(meta), path("*.fas{.gz,}"), emit: fas - 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 add = add ? "--add <(unpigz -cdf ${add})" : '' - def addfragments = addfragments ? "--addfragments <(unpigz -cdf ${addfragments})" : '' - def addfull = addfull ? "--addfull <(unpigz -cdf ${addfull})" : '' - def addprofile = addprofile ? "--addprofile <(unpigz -cdf ${addprofile})" : '' - def addlong = addlong ? "--addlong <(unpigz -cdf ${addlong})" : '' - def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.fas.gz" : "> ${prefix}.fas" - // this will not preserve MAFFTs return value, but mafft crashes when it receives a process substitution - if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!" - """ - mafft \\ - --thread ${task.cpus} \\ - ${add} \\ - ${addfragments} \\ - ${addfull} \\ - ${addprofile} \\ - ${addlong} \\ - ${args} \\ - ${fasta} \\ - ${write_output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//') - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def add = add ? "--add ${add}" : '' - def addfragments = addfragments ? "--addfragments ${addfragments}" : '' - def addfull = addfull ? "--addfull ${addfull}" : '' - def addprofile = addprofile ? "--addprofile ${addprofile}" : '' - def addlong = addlong ? "--addlong ${addlong}" : '' - if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!" - """ - touch ${prefix}.fas${compress ? '.gz' : ''} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//') - pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) - END_VERSIONS - """ - -} diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml deleted file mode 100644 index ed5e1ea3..00000000 --- a/modules/nf-core/mafft/meta.yml +++ /dev/null @@ -1,108 +0,0 @@ -name: mafft -description: Multiple sequence alignment using MAFFT -keywords: - - fasta - - msa - - multiple sequence alignment -tools: - - "mafft": - description: Multiple alignment program for amino acid or nucleotide sequences - based on fast Fourier transform - homepage: https://mafft.cbrc.jp/alignment/software/ - documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html - tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html - doi: "10.1093/nar/gkf436" - licence: ["BSD"] - identifier: biotools:MAFFT - - "pigz": - description: "Parallel implementation of the gzip algorithm." - homepage: "https://zlib.net/pigz/" - documentation: "https://zlib.net/pigz/pigz.pdf" - identifier: biotools:MAFFT -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing the sequences to align. May be gzipped or - uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - add: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` - using `--add`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfragments: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` - using `--addfragments`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfull: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` - using `--addfull`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addprofile: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` - using `--addprofile`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - meta6: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addlong: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` - using `--addlong`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. - Set to true to enable/false to disable compression. Compression is done using - pigz, and is multithreaded. -output: - - fas: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.fas{.gz,}": - type: file - description: Aligned sequences in FASTA format. May be gzipped or uncompressed. - pattern: "*.fas{.gz,}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@MillironX" -maintainers: - - "@MillironX" - - "@Joon-Klaps" diff --git a/modules/nf-core/mafft/tests/main.nf.test b/modules/nf-core/mafft/tests/main.nf.test deleted file mode 100644 index 683979f7..00000000 --- a/modules/nf-core/mafft/tests/main.nf.test +++ /dev/null @@ -1,248 +0,0 @@ -nextflow_process { - - name "Test Process MAFFT" - script "../main.nf" - process "MAFFT" - tag "modules" - tag "modules_nfcore" - tag "mafft" - - test("SARS-CoV-2 scaffolds fasta - uncompressed") { - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [[:], []] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - uncompressed")} - ) - } - - } - - test("SARS-CoV-2 scaffolds fasta - compressed") { - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [[:], []] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - compressed")} - ) - } - - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites fasta normal") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [[ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[2] = [[:], []] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta normal") } - ) - } - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites fasta fragments") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta fragments") } - ) - } - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites fasta full") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [[:], []] - input[3] = [[ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta full") } - ) - } - - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites fasta profile") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [[:], []] - input[3] = [[:], []] - input[4] = [[ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta profile") } - ) - } - - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites fasta long") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [[:], []] - input[2] = [[:], []] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta long") } - ) - } - - } - - test("SARS-CoV-2 scaffolds fasta - add informative sites all sites fasta multiple") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) - ] - input[2] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) - ] - input[3] = [[:], []] - input[4] = [[:], []] - input[5] = [[:], []] - input[6] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - add informative sites fasta multiple") } - ) - } - - } - -} \ No newline at end of file diff --git a/modules/nf-core/mafft/tests/main.nf.test.snap b/modules/nf-core/mafft/tests/main.nf.test.snap deleted file mode 100644 index c14ad086..00000000 --- a/modules/nf-core/mafft/tests/main.nf.test.snap +++ /dev/null @@ -1,250 +0,0 @@ -{ - "SARS-CoV-2 scaffolds fasta - uncompressed": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas:md5,23426611f4a0df532b6708f072bd445b" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas:md5,23426611f4a0df532b6708f072bd445b" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:08:41.735774847" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta multiple": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:10:38.940555785" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta normal": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,a57a34f1c566dea114dc1b13416536d4" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,a57a34f1c566dea114dc1b13416536d4" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:09:35.656248409" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta long": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,e8868da70d1f3050a8daaee0e53b2fd9" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,e8868da70d1f3050a8daaee0e53b2fd9" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:10:26.372655394" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta profile": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,c2b5caf39beff4473878e6aa4036ad43" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,c2b5caf39beff4473878e6aa4036ad43" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:10:14.039053212" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta fragments": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:09:49.737364197" - }, - "SARS-CoV-2 scaffolds fasta - add informative sites fasta full": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,611cb0a65195a282f110f7f56e310c66" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,611cb0a65195a282f110f7f56e310c66" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:10:02.952480822" - }, - "SARS-CoV-2 scaffolds fasta - compressed": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,23426611f4a0df532b6708f072bd445b" - ] - ], - "1": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ], - "fas": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fas.gz:md5,23426611f4a0df532b6708f072bd445b" - ] - ], - "versions": [ - "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee" - ] - } - ], - "timestamp": "2024-02-09T19:09:21.096197597" - } -} \ No newline at end of file diff --git a/modules/nf-core/mafft/tests/tags.yml b/modules/nf-core/mafft/tests/tags.yml deleted file mode 100644 index caddc3cd..00000000 --- a/modules/nf-core/mafft/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mafft: - - modules/nf-core/mafft/** diff --git a/subworkflows/local/preprocess.nf b/subworkflows/local/preprocess.nf index ef17950f..76f1bbc5 100644 --- a/subworkflows/local/preprocess.nf +++ b/subworkflows/local/preprocess.nf @@ -17,6 +17,7 @@ workflow PREPROCESS { TCOFFEE_EXTRACTFROMPDB.out.formatted_pdb .groupTuple() .set { ch_preprocessed_data } + ch_versions = ch_versions.mix(TCOFFEE_EXTRACTFROMPDB.out.versions) } emit: diff --git a/subworkflows/local/visualization.nf b/subworkflows/local/visualization.nf index c2281650..38ed7c49 100644 --- a/subworkflows/local/visualization.nf +++ b/subworkflows/local/visualization.nf @@ -35,6 +35,7 @@ workflow VISUALIZATION { FOLDMASON_CREATEDB( ch_optional_data ) + ch_versions = ch_versions.mix(FOLDMASON_CREATEDB.out.versions) ch_msa_tree_data .combine(FOLDMASON_CREATEDB.out.db.collect(), by:0) @@ -55,6 +56,7 @@ workflow VISUALIZATION { [[:],[]] ) + ch_versions = ch_versions.mix(FOLDMASON_MSA2LDDTREPORT.out.versions) ch_html = FOLDMASON_MSA2LDDTREPORT.out.html emit: