Updating nf-core modules and subworkflows, including preparation for topics by Kevin-Brockers · Pull Request #487 · nf-core/chipseq

Kevin-Brockers · 2026-03-12T13:35:54Z

PR checklist

If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,singularity --outdir <OUTDIR>).
Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).

Brief description

Adapted to topics in named workflow: ad9fa86
Updated nf-core modules, see: 2edc288
subworkflows and modules, see: b4b9757
Removed ch_version from subworkflows (local)
Changed CUSTOM_GETCHROMSIZES to SAMTOOLS_FAIDX, see: 4ddf007
a bit back and forth to fix things and run tests on a slurm cluster. I think will be fine if we squash the commits.

…nnels accordingly

github-actions · 2026-03-12T13:38:23Z

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

Posted for pipeline commit d4a562a

+| ✅ 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 2026-03-14 16:30:20

JoseEspinosa

Very nice job! Only some suggestions

CHANGELOG.md

main.nf

.nf-core.yml

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Kevin-Brockers · 2026-03-13T09:32:43Z

Shall I remove all include ... /main statements for consistency?

Kevin-Brockers added 21 commits March 11, 2026 12:00

adapt to topics channel

ad9fa86

Updated modules

2edc288

Updated subworkflows

b4b9757

updated nf-core tools

91faf07

Updated images

af5d3b1

Removed the imNotification hook, see here: nf-core/modules@f0b535b

fedb54e

local modules - bring in main.nf structure

39b1a2b

subworkflows local - main.nf structure

014bee7

Updated include statements for local subworkflows

e82085d

test if removal of ch_versions work

1a8ecb2

Removed the ch_versions from subworkflows

72ad20a

removed the ch_versions

312781d

removed ch_versions

ea8c80f

Added dummy input for optional input in SAMTOOLS_SORT

db10eb9

Debug - bring back the ch_versions

61da8fe

Replaced deprecated CUSTOM_GETCHROMSIZES to SAMTOOLS_FAIDX

22ff3e0

Added SAMTOOLS_FAIDX in favour of the CUSTOM_GETCHROMSIZES

4ddf007

Changed CUSTOM_GETCHROMSIZES -> SAMTOOLS_FAIDX and updated input cha…

6de95c8

…nnels accordingly

Initialized empty channels

21123c2

fix typo

d350b80

Changed output channel to get ch_macs_gsize right

fcab2d6

Kevin-Brockers added 4 commits March 12, 2026 15:55

fixed the remote linting

1ff9f3b

put in right file paths

0430da3

Small fixes for PR tests

c77e72d

still fixing the PR tests

84f4b8b

JoseEspinosa requested changes Mar 12, 2026

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nf-core deleted a comment from JoseEspinosa Mar 13, 2026

Kevin-Brockers and others added 2 commits March 13, 2026 10:20

Update main.nf

ee7c272

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Update .nf-core.yml

3cb3b08

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Kevin-Brockers added 2 commits March 13, 2026 10:37

Implemented comments by Jose

202785f

hopefully this helps with the nf-core lint PR tests

de80730

Kevin-Brockers changed the title ~~Dev topic channel adaptation~~ Updating nf-core modules and subworkflows, including preparation for topics Mar 13, 2026

Kevin-Brockers added the enhancement label Mar 13, 2026

Kevin-Brockers added this to Hackathon March 2026 Mar 13, 2026

Kevin-Brockers moved this to Ready for review in Hackathon March 2026 Mar 13, 2026

Kevin-Brockers moved this from Ready for review to In progress in Hackathon March 2026 Mar 13, 2026

Kevin-Brockers and others added 9 commits March 13, 2026 12:29

Updated the CHANGELOG

5be6cab

Updated container and conda env

2d0e558

Added topics

70fd6b8

updated env and topic channel

6d93aad

updated container urls

12d4c7f

updated container url

24a0b9a

updated env and topics channel

dbc44b2

upadated CHANGELOG, local module and tests

9888963

updated test snapshots

d4a562a

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Updating nf-core modules and subworkflows, including preparation for topics#487

Updating nf-core modules and subworkflows, including preparation for topics#487
Kevin-Brockers wants to merge 38 commits intonf-core:devfrom
Kevin-Brockers:dev_topic_channel_adaptation

Kevin-Brockers commented Mar 12, 2026 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Kevin-Brockers commented Mar 12, 2026 •

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