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Use --bga when creating bigWigs

Open edmundmiller opened this issue 6 months ago • 3 comments

The primary change addresses GitHub issue #468. In modules/local/bedtools_genomecov.nf, the bedtools genomecov command was updated from -bg to -bga. This ensures bigWig files include zero-coverage bins, resulting in lower background levels and improved visualization in IGV.

This change is documented in docs/output.md with an [!IMPORTANT] callout, explaining the benefits and providing a configuration example for users to revert to the -bg behavior via ext.args. The CHANGELOG.md was updated with an entry for v2.2.0dev, linking to the issue and the specific documentation section.

Additionally, several maintenance TODOs were resolved:

  • The contributors section in nextflow.config was populated with detailed information.
  • A comment in conf/base.config regarding process defaults was clarified.
  • A TODO in workflows/chipseq.nf about samplesheet validation was updated to a note referencing the nf-validation plugin.

edmundmiller avatar Jun 24 '25 19:06 edmundmiller

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1. Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

nf-core-bot avatar Jun 24 '25 19:06 nf-core-bot

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 81a2a58

+| ✅ 269 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  33 tests had warnings |!

:heavy_exclamation_mark: 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 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_if_empty_null - ifEmpty(null) found in prepare_genome.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] _
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] _
  • local_component_structure - igv.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 - 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 - bam_remove_orphans.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 - genome_blacklist_regions.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 - plot_macs3_qc.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_custom_phantompeakqualtools.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_custom_peaks.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 - star_genomegenerate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - annotate_boolean_peaks.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 - bam_peaks_call_qc_annotate_macs3_homer.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 - bam_filter_bamtools.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 - align_star.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

:grey_question: Tests ignored:

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

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-17 15:01:19

github-actions[bot] avatar Jun 24 '25 19:06 github-actions[bot]

@nf-core-bot fix linting

edmundmiller avatar Jun 24 '25 19:06 edmundmiller