[do not merge] remove isMaster block to see how it affects the matrix (master)

[adamrtalbot]

• Install kraken2 and bracken
• Change nextflow configurations
• Initial addition of kraken and bracken to pipeline
• Fix include statements
• Fix include statements
• Include module config files
• Use presence of kraken_db to determine bracken run, add save params
• Fix multiqc for Bracken/Kraken
• Add Bracken/Kraken citations
• Fix bracken config
• Update bracken
• Adjust multiqc configs for updated bracken
• Add input validation and update scheme
• Change default Bracken precision to species
• Debug input validation
• Documentation/output image
• Update changelog
• Update Kraken2 module
• Linting
• Change to --contaminant_screening param
• Fixing save unaligned default
• Debugging
• Update usage
• Provide motivation for Kraken2 parameters
• Fix typo
• Update metro map
• Update schema
• Update docs/usage.md
• Change output directory for kraken2/bracken
• Update main.nf
• Update Changelog
• Another changelog fix
• Update CHANGELOG.md
• Linting fix
• make snapshot versions pretty
• update CHANGELOG
• update all snapshots
• update half of all snaps
• more snapshots
• update snapshots
• update snapshots
• Update CHANGELOG.md
• update snapshots
• do not sort output
• sort output by PATH
• nf-core pipelines bump-version 3.16.0dev
• update snapshots
• update CHANGELOG
• Update CHANGELOG.md
• snapshot more files
• snapshot more files
• feature counts snapshots
• typo
• more snapshots
• more snapshots
• update snapshots
• better regex
• fix regex
• better regex
• update snapshot
• code polish
• rescue some snaps
• Apply suggestions from code review
• tiny refactor part I
• tiny refactor part II - IT IS GROOVY WE CAN SUBSTRACT 🤦
• update regexes
• move pipeline regexes in UTILS_PIPELINE
• simplify regexes
• fix regexes
• Merge conflcits
• Update hisat2 patch
• (Hopefully) final linting fix
• Change PR number
• snapshots all filenames
• code polish
• typo
• Apply suggestions from code review
• update CHANGELOG
• update animated metro_map
• no snpashots of tasks size for workflow for remove_ribo_rna
• snapshot number of sucessful tasks
• typo
• Update tests/featurecounts_group_type.nf.test
• why was this not commited?
• patch bedtools/genomecov to use quay.io to solve issue with nf-core download
• use url for singularity
• use proper url for singularity
• prepare RC 3.15.2
• update version in snapshots too
• use nft-utils
• update nftignore
• update pipeline versions in snapshot
• update CHANGELOG
• update nftignore
• update nftignore
• 3.16.0 instead of 3.15.2
• Update CHANGELOG.md
• use nft-utils 0.0.2 to get relative path in snapshots
• forgot a merge
• Apply suggestions from code review
• nf-core pipelines bump-version 3.17.0dev
• Bump version in CHANGELOG
• Bump versions in snap
• Template update for nf-core/tools version 3.0.0
• Template update for nf-core/tools version 3.0.1
• fix merge conflicts
• Apply suggestions from code review
• fix nf-core lint
• install nf-test 0.9.0
• install nf-test once only
• use proper Channel factory
• rename function test
• fix align
• fix samplesheet usage
• fix tests
• fix tests
• update CHANGELOG
• Apply suggestions from code review
• update test adjacent files
• clean nftignore for kallisto
• minor code polish
• kallisto: update snapshots
• update plugin version
• update nftignore
• update fastq_fastqc_umitools_trimgalore
• update nftignore and snapshots for salmon and kallisto
• no set -C until we fix modules upstream
• update nftignore
• update default tests
• update featurecounts_group_type tests
• update nftignore and hisat2 snapshots
• update min_mapped_reads snapshots
• do not snapshot the bam
• update remove_ribo_rna tests
• update skip_qc tests
• update skip_trimming snapshots
• Update subworkflow to fix variable
• update changelog
• update last snapshots
• ignore file
• Correct CHANGELOG
• only one samplesheetToList
• update CHANGELOG
• Template update for nf-core/tools version 3.0.2
• fix GHA
• fix GHA
• fix GHA
• fix snapshots
• :shakefist:
• Fix ifEmpty() issues with trimming
• Update CHANGELOG
• Update rnaseq prepro
• Reset versions back to 3.16.1 for patch release
• Update changelog
• disable conda pipeline level tests + update CHANGELOG
• fix PR link
• Properly disable conda pipeline level tests
• Update CHANGELOG.md
• Bump versions back to 3.17.0 after release
• Update CHANGELOG
• Prettier
• appy changes for ARM
• Fix up config
• Reset environment ymls
• Reset main.nfs with software changes only
• Link sw configs to arm profile
• Add process block
• note pins
• Remove conda overrides that were having no impact
• Use different RSEQC pin
• update BEDGRAPHTOBIGWIG pin
• Fix annotation
• Don't think we need the RSEQC pin
• correct ucsc
• Triage arm deps
• Non-igenomes STAR can use the latest star
• remove rogue comment
• update arm conf
• Bump lots of modules so that conda versions have arm builds
• Update prepare_genome snaps
• Update align_star snaps
• Update quantify_rsem snaps
• [skip ci] First batch of pipeline test updates
• [skip ci] Update subworkflow snaps due to patch on module
• [skip ci] bump remove_ribo_rna snaps
• [skip ci] Update snaps for --pseudo_aligner salmon --skip_qc --skip_alignment
• [skip ci] update star_rsem pipeline snaps
• [skip ci] update pipeline tests for skip_qc
• update skip_trimming snaps
• update changelog
• Revert hisat diff
• remove excess newlines
• Bump star modules
• Update option for new STAR
• Fix up pipeline tests
• Fix local star swf to match star
• update changelog
• patch sortmerna to 4.3.7 in seqera channel pending a functional verison appearing in conda-forge
• Update changelog
• fix sortmerna tests for order
• update a relevant pipeline test
• Cut out module redundant software overrides
• Add frozen ARM builds
• Container directives for conda overrides
• Temporary Trimgalore override, singularity fixes for rsem processes
• update docs
• Fix argument conflict between STAR versions
• Fix config error
• Correction to star rsem
• Refine config setup
• Bump trimgalore module
• Fix up ARM profile for updated trim-galore
• Apply suggestions from code review
• Apply suggestions from code review
• Add notes for kraken2/ braken
• Update docs
• prettier
• lint fix
• [skip ci] Reorg ARM bits
• Update arm.config
• Fix syntax error
• revert trimgalore tweak to appease linter
• Update pipeline-level tests
• Update CHANGELOG
• Bump versions
• update changelog
• update CHANGELOG
• update and patch modules
• Remove isMaster block from CI

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @adamrtalbot,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0acaeb4

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: assets/multiqc_config.yml
• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

• files_exist - File is ignored: conf/modules.config
• nextflow_config - Config default ignored: params.ribo_database_manifest
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
• multiqc_config - multiqc_config
• modules_config - modules_config

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-rnaseq_logo_light.png
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-rnaseq_logo_light.png
• files_exist - File found: docs/images/nf-core-rnaseq_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: main.nf
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.config
• files_exist - File found: modules.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-rnaseq_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowRnaseq.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: validation.help.beforeText
• nextflow_config - Config variable found: validation.help.afterText
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable found: validation.summary.beforeText
• nextflow_config - Config variable found: validation.summary.afterText
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 3.17.0
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
• nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
• nextflow_config - Config default value correct: params.gtf_group_features= gene_id
• nextflow_config - Config default value correct: params.featurecounts_group_type= gene_biotype
• nextflow_config - Config default value correct: params.featurecounts_feature_type= exon
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.trimmer= trimgalore
• nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
• nextflow_config - Config default value correct: params.umitools_extract_method= string
• nextflow_config - Config default value correct: params.umitools_grouping_method= directional
• nextflow_config - Config default value correct: params.aligner= star_salmon
• nextflow_config - Config default value correct: params.pseudo_aligner_kmer_size= 31
• nextflow_config - Config default value correct: params.min_mapped_reads= 5.0
• nextflow_config - Config default value correct: params.kallisto_quant_fraglen= 200
• nextflow_config - Config default value correct: params.kallisto_quant_fraglen_sd= 200
• nextflow_config - Config default value correct: params.stranded_threshold= 0.8
• nextflow_config - Config default value correct: params.unstranded_threshold= 0.1
• nextflow_config - Config default value correct: params.deseq2_vst= true
• nextflow_config - Config default value correct: params.rseqc_modules= bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
• nextflow_config - Config default value correct: params.bracken_precision= S
• nextflow_config - Config default value correct: params.skip_bbsplit= true
• nextflow_config - Config default value correct: params.skip_preseq= true
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-rnaseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-rnaseq_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-rnaseq_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
• version_consistency - Version tags are numeric and consistent between container, release tag and config.
• included_configs - Pipeline config includes custom configs.

Run details

• nf-core/tools version 3.0.2
• Run at 2024-10-23 17:09:44