nf-core_modules/modules/msisensor/msi/main.nf
Mahesh Binzer-Panchal d473a247d2
Replace remaining task.ext.suffix with task.ext.prefix (#1117)
* Replace remaining task.ext.suffix with task.ext.prefix
2021-12-07 15:00:43 +01:00

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1.3 KiB
Text

process MSISENSOR_MSI {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' :
'quay.io/biocontainers/msisensor:0.5--hb3646a4_2' }"
input:
tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers)
output:
tuple val(meta), path("${prefix}") , emit: output
tuple val(meta), path("${prefix}_dis") , emit: output_dis
tuple val(meta), path("${prefix}_germline"), emit: output_germline
tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
msisensor \\
msi \\
-d $homopolymers \\
-n $normal_bam \\
-t $tumor_bam \\
-o $prefix \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
msisensor: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
END_VERSIONS
"""
}