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Fix "Markdups process marks aligner output as markdups output incorrectly" #105

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merged 4 commits into from
Oct 30, 2024
Merged

Fix "Markdups process marks aligner output as markdups output incorrectly" #105

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2ffdf56
Do not emit aligner input bams as markdups outputs
mvanniekerkHartwig Oct 17, 2024
d64a54f
fix markdups bai file pattern
mvanniekerkHartwig Oct 18, 2024
08c083b
Merge branch 'dev' into fix-markdups-output
scwatts Oct 29, 2024
52064e8
Update CHANGELOG.md
scwatts Oct 29, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)

## [dev]

- [105](https://github.com/nf-core/oncoanalyser/pull/105) - Adjust MarkDups outputs to improve efficiency with k8s
- [98](https://github.com/nf-core/oncoanalyser/pull/98) - Fix typos in error messages for process and run mode check
- [96](https://github.com/nf-core/oncoanalyser/pull/96) - Added missing type field to an entry in the nextflow_schema.json
- [95](https://github.com/nf-core/oncoanalyser/pull/95) - Post-release bump
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4 changes: 2 additions & 2 deletions modules/local/markdups/main.nf
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Expand Up @@ -17,8 +17,8 @@ process MARKDUPS {
val has_umis

output:
tuple val(meta), path('*bam'), path('*bai'), emit: bam
path 'versions.yml' , emit: versions
tuple val(meta), path('*.markdups.bam'), path('*.markdups.bam.bai'), emit: bam
path 'versions.yml' , emit: versions
path '*.tsv'

when:
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