Update aligners (bwa, bowtie2, chromap and star) by Kevin-Brockers · Pull Request #523 · nf-core/chipseq

Kevin-Brockers · 2026-07-08T08:05:01Z

This is a bit of a bigger PR - see here: #522

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
CHANGELOG.md is updated.

…ch_fasta_fai dummy maps to match updated nf-core maintained samtools components

Kevin-Brockers · 2026-07-08T08:07:32Z

I'm currently fixing a few more things - e.g: when using chromap the pipeline currently fails since chromap does not add readgroups by default and picard markduplicates currently fails.

I'm on it see here: nf-core/modules#12283

Therefore the tests are currently failing

github-actions · 2026-07-08T08:07:52Z

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

Posted for pipeline commit 44328ed

+| ✅ 271 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   8 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 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
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

❔ Tests ignored:

nextflow_config - Config default ignored: params.bamtools_filter_pe_config
nextflow_config - Config default ignored: params.bamtools_filter_se_config
files_unchanged - File ignored due to lint config: assets/nf-core-chipseq_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-chipseq_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
merge_markers - Ignoring file /home/runner/work/chipseq/chipseq/modules/nf-core/bowtie2/align/tests/main.nf.test.snap

✅ 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/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/CONTRIBUTING.md
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.skip_preseq= true
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/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_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/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/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/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/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/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/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 - docs/images/nf-core-chipseq_logo_light.png matches the template
files_unchanged - docs/README.md 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: 25.10.4, Config: 25.10.4
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: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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 - SAMTOOLS_FAIDX 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: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.0.2
Run at 2026-07-08 22:25:23

JoseEspinosa

Just a small question and a suggestion for the fastq_align_chromap for the nf-core subworkflow

JoseEspinosa · 2026-07-14T21:39:07Z

+    //
+    // Update read groups
+    //
+    PICARD_ADDORREPLACEREADGROUPS(CHROMAP_CHROMAP.out.bam, ch_fasta_fai)


This is maybe a comment more for the subworkflows that does not belong here, but this will be always run regardless of whether add_readgroups is set to false

Although, in this pipeline does not have any relevance as it is always true, to be fair

JoseEspinosa · 2026-07-14T21:48:14Z

    - config_defaults:
        - params.bamtools_filter_se_config
        - params.bamtools_filter_pe_config
+  merge_markers:


Why this is needed?

Kevin-Brockers added 17 commits July 6, 2026 15:06

updated modules

1864187

updated subworkflows

4579582

updated modules

64ea282

Updated ro-crate-metadata

9842343

Updated local subworkflow to work with updated nf-core components

2ae9d90

updated channels to match nf-core components for bowtie2

75f07ae

Updated bowtie2

97cc718

Updated bwa

cd996f5

Fix bwa to match updated nf-core components

d204cce

updated chromap modules and subworkflows

d7894bd

Updated nf-core components

2ba03f8

Updated chromap aligner to match updated nf-core components

c7b8711

removed versions.yml when topics channel is used

8c8fc69

version dump bwa and chromap

159b5a3

updated - changed branch operator to a typed channel operator, added …

691caeb

…ch_fasta_fai dummy maps to match updated nf-core maintained samtools components

minor updates

e121727

fix the local align_star subworkflow

bf4b49f

Kevin-Brockers mentioned this pull request Jul 8, 2026

implemented readgroup addition in fastq_align_chromap, since chromap has no option to do it nf-core/modules#12283

Merged

8 tasks

Kevin-Brockers added 5 commits July 8, 2026 12:31

hotfix to pass testing conflicts

ea8d3d6

Updated bowtie2 snapshot

17d5544

Updated snapshot

84c5250

Updated snapshot

d398734

Updated snaptshot

3489c5a

Kevin-Brockers changed the title ~~Update aligner (bwa, bowtie2 and chromap)~~ Update aligners (bwa, bowtie2 and chromap) Jul 8, 2026

Kevin-Brockers added 4 commits July 8, 2026 15:52

Updated bowtie2 snapshot

6f0d6fa

Updated snapshot

715adde

updated snapshot

f4ce070

Updated nf-core components and installed new tool

9353178

Kevin-Brockers added 5 commits July 8, 2026 17:34

fixed read groups when using chromap aligner

740b864

Fixed the star aligner

2fd8364

Excluded multiqc output

ce93842

Updated nftignore

c62223e

Updated snapshots

44328ed

Kevin-Brockers changed the title ~~Update aligners (bwa, bowtie2 and chromap)~~ Update aligners (bwa, bowtie2, chromap and star) Jul 8, 2026

Kevin-Brockers marked this pull request as ready for review July 8, 2026 22:52

Kevin-Brockers linked an issue Jul 14, 2026 that may be closed by this pull request

Update the aligners (bowtie2, bwa, chromap and star) and associated steps processing steps to use topics channel for software versions. #522

Open

JoseEspinosa approved these changes Jul 14, 2026

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Update aligners (bwa, bowtie2, chromap and star)#523

Update aligners (bwa, bowtie2, chromap and star)#523
Kevin-Brockers wants to merge 31 commits into
nf-core:devfrom
Kevin-Brockers:update_aligner

Kevin-Brockers commented Jul 8, 2026 •

edited

Loading

Uh oh!

Kevin-Brockers commented Jul 8, 2026

Uh oh!

github-actions Bot commented Jul 8, 2026 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

JoseEspinosa left a comment

Uh oh!

JoseEspinosa Jul 14, 2026

Uh oh!

JoseEspinosa Jul 14, 2026

Uh oh!

JoseEspinosa Jul 14, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Uh oh!

Conversation

Kevin-Brockers commented Jul 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

PR checklist

Uh oh!

Kevin-Brockers commented Jul 8, 2026

Uh oh!

github-actions Bot commented Jul 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

JoseEspinosa left a comment

Choose a reason for hiding this comment

Uh oh!

JoseEspinosa Jul 14, 2026

Choose a reason for hiding this comment

Uh oh!

JoseEspinosa Jul 14, 2026

Choose a reason for hiding this comment

Uh oh!

JoseEspinosa Jul 14, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Kevin-Brockers commented Jul 8, 2026 •

edited

Loading

github-actions Bot commented Jul 8, 2026 •

edited

Loading

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