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Merge-template-3.5.1#434

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JoseEspinosa merged 7 commits intonf-core:devfrom
JoseEspinosa:merge-template-3.5.1
Nov 20, 2025
Merged

Merge-template-3.5.1#434
JoseEspinosa merged 7 commits intonf-core:devfrom
JoseEspinosa:merge-template-3.5.1

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@JoseEspinosa JoseEspinosa commented Nov 20, 2025

Merge template 3.5.1

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github-actions bot commented Nov 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b463db6

+| ✅ 268 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  38 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 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
  • 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 nextflow.config: Specify any additional parameters here
  • 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 ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/atacseq/atacseq/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • local_component_structure - gtf2bed.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 - igv.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 - 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 - deseq2_qc.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 - bamtools_filter.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 - genome_blacklist_regions.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 - star_genomegenerate.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 - macs3_consensus.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 - get_autosomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - tss_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_shift_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/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 - bigwig_plot_deeptools.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_filter_bamtools.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 - input_check.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

❔ 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 2025-11-20 11:24:02

@JoseEspinosa JoseEspinosa merged commit c7b9e7b into nf-core:dev Nov 20, 2025
48 of 52 checks passed
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@maxulysse maxulysse maxulysse approved these changes

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@JoseEspinosa @maxulysse @nf-core-bot