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modify markduplicates module (#681)

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* tested

* updated meta config and test config
This commit is contained in:
Mei Wu 2021-09-15 11:02:28 +02:00 committed by GitHub
parent c485109d9b
commit b2a6f5409e
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3 changed files with 49 additions and 44 deletions
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7
modules/picard/markduplicates/main.nf
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@ -23,6 +23,7 @@ process PICARD_MARKDUPLICATES {
output: output:
tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bai") , optional:true, emit: bai
tuple val(meta), path("*.metrics.txt"), emit: metrics tuple val(meta), path("*.metrics.txt"), emit: metrics
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
@ -40,9 +41,9 @@ process PICARD_MARKDUPLICATES {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
MarkDuplicates \\ MarkDuplicates \\
$options.args \\ $options.args \\
INPUT=$bam \\ -I $bam \\
OUTPUT=${prefix}.bam \\ -O ${prefix}.bam \\
METRICS_FILE=${prefix}.MarkDuplicates.metrics.txt -M ${prefix}.MarkDuplicates.metrics.txt
echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
""" """

5
modules/picard/markduplicates/meta.yml
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@ -34,6 +34,10 @@ output:
type: file type: file
description: BAM file with duplicate reads marked/removed description: BAM file with duplicate reads marked/removed
pattern: "*.{bam}" pattern: "*.{bam}"
- bai:
type: file
description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag
pattern: "*.{bai}"
- metrics: - metrics:
type: file type: file
description: Duplicate metrics file generated by picard description: Duplicate metrics file generated by picard
@ -44,3 +48,4 @@ output:
pattern: "*.{version.txt}" pattern: "*.{version.txt}"
authors: authors:
- "@drpatelh" - "@drpatelh"
- "@projectoriented"

3
tests/modules/picard/markduplicates/test.yml
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@ -6,8 +6,7 @@
files: files:
- path: ./output/picard/test.MarkDuplicates.metrics.txt - path: ./output/picard/test.MarkDuplicates.metrics.txt
- path: ./output/picard/test.bam - path: ./output/picard/test.bam
md5sum: 3270bb142039e86aaf2ab83c540225d5 md5sum: b520ccdc3a9edf3c6a314983752881f2
- name: picard markduplicates on unsorted bam - name: picard markduplicates on unsorted bam
command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
tags: tags: