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picard CollectWgsMetrics: update to new cli args (#1578)

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* update to new cli args

* remove bam index from tuple, not needed by program

* bump picard version

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
This commit is contained in:
Matthias De Smet 2022-04-29 09:32:32 +02:00 committed by GitHub
parent b3e9b88e80
commit ec10f98d55
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2 changed files with 8 additions and 9 deletions
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14
modules/picard/collectwgsmetrics/main.nf
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@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null) conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam)
path fasta path fasta
output: output:
@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
CollectWgsMetrics \\ CollectWgsMetrics \\
$args \\ $args \\
INPUT=$bam \\ -INPUT $bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\ -OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta -REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

3
tests/modules/picard/collectwgsmetrics/main.nf
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@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
workflow test_picard_collectwgsmetrics { workflow test_picard_collectwgsmetrics {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)