Fix strict syntax errors by bentsherman · Pull Request #491 · nf-core/chipseq

bentsherman · 2026-03-19T03:59:00Z

Hi, just testing the pipeline with strict syntax for Nextflow 26.04. Feel free to take these changes if they make sense

NOTE: nf-core modules and subworkflows can be fixed properly by just updating them from nf-core/modules

github-actions · 2026-03-19T04:01:59Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 0c65ff9

+| ✅ 266 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
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
pipeline_todos - TODO string in base.config: Check the defaults for all processes
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!

❔ Tests ignored:

nextflow_config - Config default ignored: params.bamtools_filter_pe_config
nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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-chipseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-chipseq_logo_light.png
files_exist - File found: docs/images/nf-core-chipseq_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: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.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-chipseq_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/WorkflowChipseq.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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 ends in dev: 2.2.0dev
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.fragment_size= 200
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.aligner= bwa
nextflow_config - Config default value correct: params.broad_cutoff= 0.1
nextflow_config - Config default value correct: params.min_reps_consensus= 1
nextflow_config - Config default value correct: params.deseq2_vst= 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.fingerprint_bins= 500000
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/
nf_test_content - 'tests/chromap.nf.test' contains outdir parameter
nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chromap.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' contains outdir parameter
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
nf_test_content - 'tests/bowtie2.nf.test' contains outdir parameter
nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bowtie2.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-chipseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-chipseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-chipseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
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: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.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
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - KHMER_UNIQUEKMERS found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - GTF2BED found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_BLACKLIST_REGIONS found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - CHROMAP_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - CHROMAP_CHROMAP found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MERGESAMFILES found in conf/modules.config and Nextflow scripts.
modules_config - BAMTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
modules_config - BAM_REMOVE_ORPHANS found in conf/modules.config and Nextflow scripts.
modules_config - PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTMULTIPLEMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_COMPUTEMATRIX found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_PLOTPROFILE found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_PLOTHEATMAP found in conf/modules.config and Nextflow scripts.
modules_config - DEEPTOOLS_PLOTFINGERPRINT found in conf/modules.config and Nextflow scripts.
modules_config - MACS3_CALLPEAK found in conf/modules.config and Nextflow scripts.
modules_config - FRIP_SCORE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_CUSTOM_PEAKS found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_MACS3_QC found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_HOMER_ANNOTATEPEAKS found in conf/modules.config and Nextflow scripts.
modules_config - MACS3_CONSENSUS found in conf/modules.config and Nextflow scripts.
modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - ANNOTATE_BOOLEAN_PEAKS found in conf/modules.config and Nextflow scripts.
modules_config - DESEQ2_QC found in conf/modules.config and Nextflow scripts.
modules_config - IGV found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-19 15:02:08

JoseEspinosa · 2026-03-19T11:15:48Z

Thanks @bentsherman! Actually, we are working with @Kevin-Brockers in updating modules, so I think it would make sense to wait until #487 is merged to update this PR

JoseEspinosa

LGTM! Thanks @bentsherman ❤️

bentsherman requested a review from JoseEspinosa March 19, 2026 03:59

Fix strict syntax errors

0c65ff9

bentsherman force-pushed the fix-strict-syntax branch from aa0125b to 0c65ff9 Compare March 19, 2026 14:59

JoseEspinosa approved these changes Mar 19, 2026

View reviewed changes

JoseEspinosa merged commit d8b98cd into dev Mar 19, 2026
20 checks passed

ewels deleted the fix-strict-syntax branch March 19, 2026 17:19

Kevin-Brockers mentioned this pull request Apr 1, 2026

strict syntax - language update #485

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Fix strict syntax errors#491

Fix strict syntax errors#491
JoseEspinosa merged 1 commit intodevfrom
fix-strict-syntax

bentsherman commented Mar 19, 2026

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github-actions Bot commented Mar 19, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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bentsherman commented Mar 19, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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JoseEspinosa commented Mar 19, 2026

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github-actions Bot commented Mar 19, 2026 •

edited

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️