8000 Use --bga when creating bigWigs by edmundmiller · Pull Request #470 · nf-core/chipseq · GitHub
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Use --bga when creating bigWigs #470

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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 edmundmiller added this to the 2.2 milestone Jun 24, 2025
@edmundmiller edmundmiller self-assigned this Jun 24, 2025
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Pull Request Overview

This PR fixes GitHub issue #468 by updating the bedtools genomecov command to use the -bga option, which includes zero-coverage bins for improved bigWig output and visualization in IGV. The changes also update documentation, contributor details, and in-code comments for clarity and maintainability.

  • Updated the bedtools command in modules/local/bedtools_genomecov.nf from -bg to -bga.
  • Revised documentation in docs/output.md to explain the change and configuration override.
  • Updated contributor information in nextflow.config and modified comments in workflows/chipseq.nf and conf/base.config.

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.

Show a summary per file
File Description
workflows/chipseq.nf Updated sample sheet validation comment to suggest nf-validation plugin usage
nextflow.config Revised contributor details with complete information
modules/local/bedtools_genomecov.nf Changed the bedtools command option from -bg to -bga to improve visualization
docs/output.md Added an [!IMPORTANT] note detailing the change and how to override it
conf/base.config Clarified the process defaults comment for enhanced clarity
CHANGELOG.md Documented the changes made in version v2.2.0dev

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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.

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github-actions bot commented Jun 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit edc561d

+| ✅ 236 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  31 tests had warnings |!

❗ 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 ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-chipseq_logo_dark.png">\n <img alt="nf-core/chipseq" src="docs/images/nf-core-chipseq_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/chipseq is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/chipseq \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/chipseq was originally written by Espinosa-Carrasco J, Patel H, Wang C, Ewels P.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #chipseq channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/chipseq for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • local_component_structure - macs3_consensus.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 - bedtools_genomecov.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 - genome_blacklist_regions.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 - bamtools_filter.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 - star_genomegenerate.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 - multiqc.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 - samplesheet_check.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 - frip_score.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 - multiqc_custom_phantompeakqualtools.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 - bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.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_bedgraph_bigwig_bedtools_ucsc.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

❔ 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 3.2.1
  • Run at 2025-06-24 19:59:02

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@nf-core-bot fix linting

@edmundmiller edmundmiller changed the title Fix issue in nf-core/chipseq Use --bga when creating bigWigs Jun 25, 2025
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