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Follow up #436#437

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JoseEspinosa merged 7 commits intonf-core:devfrom
JoseEspinosa:updates
Mar 24, 2026
Merged

Follow up #436#437
JoseEspinosa merged 7 commits intonf-core:devfrom
JoseEspinosa:updates

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@JoseEspinosa JoseEspinosa commented Mar 20, 2026

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/atacseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

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github-actions bot commented Mar 20, 2026

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 @JoseEspinosa,

It looks like this pull-request is has been made against the JoseEspinosa/nf-core-atacseq 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 JoseEspinosa/nf-core-atacseq 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!

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github-actions bot commented Mar 20, 2026 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a337aa5

+| ✅ 268 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  37 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 nextflow.config: Specify any additional parameters here
  • 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!
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/atacseq/atacseq/subworkflows/local/prepare_genome.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • local_component_structure - tss_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_genomegenerate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_macs3_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - get_autosomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_homer_annotatepeaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - igv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - macs3_consensus.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bamtools_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_remove_orphans.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bedtools_genomecov.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_custom_peaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genome_blacklist_regions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - frip_score.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - deseq2_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_star.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_peaks_call_qc_annotate_macs3_homer.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_bedgraph_bigwig_bedtools_ucsc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bigwig_plot_deeptools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_filter_bamtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_shift_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-23 20:51:14

@JoseEspinosa JoseEspinosa changed the base branch from master to dev March 20, 2026 16:36
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JoseEspinosa commented Mar 23, 2026

Hi @bentsherman
Just updating the module and subworkflow from nf-core as a follow-up to your PR #436 to fix strict syntax errors.

@JoseEspinosa JoseEspinosa merged commit 0a5dea1 into nf-core:dev Mar 24, 2026
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@bentsherman bentsherman bentsherman approved these changes

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@JoseEspinosa @bentsherman