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Sort peak QC plot inputs deterministically #454

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Merged
Kevin-Brockers merged 3 commits into from
Aug 22, 2026
Merged

Sort peak QC plot inputs deterministically #454

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7a89066
Sort peak QC plot inputs deterministically
NicoDeVeaux Aug 21, 2026
f5a1bca
Add CHANGELOG entry for #454
NicoDeVeaux Aug 21, 2026
b8039eb
Sort the plot inputs inside the modules instead of the channel
NicoDeVeaux Aug 21, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#438](https://github.com/nf-core/atacseq/issues/438)] - Add `checkIfExists` to file inputs in `PREPARE_GENOME` and prevent S3 access errors during index validation.
- [[PR #443](https://github.com/nf-core/atacseq/pull/443)] - Updated pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2)
- [[PR #453](https://github.com/nf-core/atacseq/pull/453)] - Updated pipeline template to [nf-core/tools 4.0.3](https://github.com/nf-core/tools/releases/tag/4.0.3)
- [[PR #454](https://github.com/nf-core/atacseq/pull/454)] - Sort the peak QC plot inputs by file name so that `PLOT_MACS3_QC` and `PLOT_HOMER_ANNOTATEPEAKS` outputs no longer depend on task completion order.

### Parameters

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6 changes: 4 additions & 2 deletions modules/local/plot_homer_annotatepeaks.nf
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@Kevin-Brockers Kevin-Brockers Aug 22, 2026

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Now it's fully reproducible ;)

Thank you, even though I feel that this is to much.

Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,12 @@ process PLOT_HOMER_ANNOTATEPEAKS {
script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "annotatepeaks"
// Files arrive in task-completion order; sort so sample order in the outputs is reproducible.
def anno_list = annos.toSorted { anno -> anno.name }.join(',')
"""
plot_homer_annotatepeaks.r \\
-i ${annos.join(',')} \\
-s ${annos.join(',').replaceAll("${suffix}","")} \\
-i ${anno_list} \\
-s ${anno_list.replaceAll("${suffix}","")} \\
-p $prefix \\
$args

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6 changes: 4 additions & 2 deletions modules/local/plot_macs3_qc.nf
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Expand Up @@ -21,10 +21,12 @@ process PLOT_MACS3_QC {
script: // This script is bundled with the pipeline, in nf-core/atacseq/bin/
def args = task.ext.args ?: ''
def peak_type = is_narrow_peak ? 'narrowPeak' : 'broadPeak'
// Files arrive in task-completion order; sort so sample order in the outputs is reproducible.
def peak_list = peaks.toSorted { peak -> peak.name }.join(',')
"""
plot_macs3_qc.r \\
-i ${peaks.join(',')} \\
-s ${peaks.join(',').replaceAll("_peaks.${peak_type}","")} \\
-i ${peak_list} \\
-s ${peak_list.replaceAll("_peaks.${peak_type}","")} \\
$args

cat <<-END_VERSIONS > versions.yml
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