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 """ }