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Fix picard markduplicates (#1084)

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* Fix picard/markduplicates with new options syntax

* Delete md5sum for bam files and add contains for metrics.txt

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
This commit is contained in:
Jose Espinosa-Carrasco 2021-11-18 21:54:14 +01:00 committed by GitHub
parent 43a1c1c6d1
commit 4e5b6ed843
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 8 additions and 6 deletions
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6
modules/picard/markduplicates/main.nf
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@ -40,9 +40,9 @@ process PICARD_MARKDUPLICATES {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
MarkDuplicates \\ MarkDuplicates \\
$options.args \\ $options.args \\
-I $bam \\ I=$bam \\
-O ${prefix}.bam \\ O=${prefix}.bam \\
-M ${prefix}.MarkDuplicates.metrics.txt M=${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}: ${getProcessName(task.process)}:

2
tests/modules/picard/markduplicates/main.nf
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@ -3,7 +3,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] ) include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : '--ASSUME_SORT_ORDER queryname' ] ) include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : 'ASSUME_SORT_ORDER=queryname' ] )
workflow test_picard_markduplicates_sorted_bam { workflow test_picard_markduplicates_sorted_bam {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map

6
tests/modules/picard/markduplicates/test.yml
View file

@ -5,8 +5,9 @@
- picard/markduplicates - picard/markduplicates
files: files:
- path: ./output/picard/test.MarkDuplicates.metrics.txt - path: ./output/picard/test.MarkDuplicates.metrics.txt
contains:
- "1.0 97 97"
- path: ./output/picard/test.bam - path: ./output/picard/test.bam
md5sum: b520ccdc3a9edf3c6a314983752881f2
- name: picard markduplicates unsorted bam - name: picard markduplicates 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:
@ -14,6 +15,7 @@
- picard/markduplicates - picard/markduplicates
files: files:
- path: ./output/picard/test.MarkDuplicates.metrics.txt - path: ./output/picard/test.MarkDuplicates.metrics.txt
contains:
- "1.0 97 97"
- path: ./output/picard/test.bam - path: ./output/picard/test.bam
md5sum: 46a6fc76048ba801d328f869ac9db020