adding homer merge peaks, and a peakcalling workflow #9172
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Pull Request Overview
This PR adds a comprehensive HOMER peak calling subworkflow with optional peak merging and annotation capabilities. The workflow builds on the existing HOMER modules to create a complete peak calling pipeline that can merge peaks across samples and annotate them with genomic features.
Key changes include:
- Added a new HOMER_MERGEPEAKS module for merging peak files across samples
- Created the HOMER_PEAKCALLING subworkflow that integrates multiple HOMER modules
- Updated HOMER version from 4.11 to 5.1 in the new components
Reviewed Changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| modules/nf-core/homer/mergepeaks/main.nf | New module implementing peak merging functionality |
| modules/nf-core/homer/mergepeaks/meta.yml | Module metadata for the mergepeaks module |
| modules/nf-core/homer/mergepeaks/environment.yml | Conda environment specification with HOMER 5.1 |
| modules/nf-core/homer/mergepeaks/tests/ | Test files for the mergepeaks module |
| subworkflows/nf-core/homer_peakcalling/main.nf | Main subworkflow implementing complete peak calling pipeline |
| subworkflows/nf-core/homer_peakcalling/meta.yml | Subworkflow metadata and documentation |
| subworkflows/nf-core/homer_peakcalling/tests/ | Test files for the complete subworkflow |
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" |
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The stub section uses a different default prefix pattern than the main script. The main script uses ${meta.id}_merged_peaks while the stub uses just ${meta.id}, which could cause inconsistent behavior between normal execution and stub mode.
| def prefix = task.ext.prefix ?: "${meta.id}" | |
| def prefix = task.ext.prefix ?: "${meta.id}_merged_peaks" |
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| annotate_individual // val: boolean - whether to annotate individual peak files | ||
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| main: | ||
| if(!gtf && annotate_individual){ |
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[nitpick] Missing space after 'if' keyword. Should be if (!gtf && annotate_individual) { to follow standard Groovy/Nextflow formatting conventions.
| if(!gtf && annotate_individual){ | |
| if (!gtf && annotate_individual) { |
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| ch_merged_peaks = HOMER_MERGEPEAKS.out.txt | ||
| ch_versions = ch_versions.mix(HOMER_MERGEPEAKS.out.versions) | ||
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| if(gtf){ |
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[nitpick] Missing space after 'if' keyword. Should be if (gtf) { to follow standard Groovy/Nextflow formatting conventions.
| if(gtf){ | |
| if (gtf) { |
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…ut to homer/findpeaks. homer_peakcalling covers all styles
1 participant
I needed a peak calling subworkflow for Homer that included annotation and MergePeaks.
This pull adds the homer MergePeaks module. It makes a couple modification to homer_groseq to include the MergePeaks step, and optional annotation.
Thought I'd offer it up -- @edmundmiller , if you're interested, this should function the same as homer_groseq if you pass in an empty channel for the gtf and set merge_peaks to
false.Homer also has a major version update (currently most homer modules are 4.11, current is 5.1). If there is any interest in merging this into homer_groseq, then I'd be happy to update the other homer modules, also.