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