process NGSCHECKMATE_NCM { label 'process_low' conda (params.enable_conda ? "bioconda::ngscheckmate=1.0.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3': 'quay.io/biocontainers/ngscheckmate:1.0.0--py27r41hdfd78af_3' }" input: path files path snp_bed path fasta output: path "*.pdf" , emit: pdf path "*_corr_matrix.txt", emit: corr_matrix path "*_matched.txt" , emit: matched path "*_all.txt" , emit: all path "*.vcf" , emit: vcfs, optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "output" def unzip = files.any { it.toString().endsWith(".vcf.gz") } """ if $unzip then for VCFGZ in *.vcf.gz; do gunzip -cdf \$VCFGZ > \$( basename \$VCFGZ .gz ); done fi NCM_REF="./"${fasta} ncm.py -d . -bed ${snp_bed} -O . -N ${prefix} $args if $unzip then rm -f *.vcf # clean up decompressed vcfs fi cat <<-END_VERSIONS > versions.yml "${task.process}": ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g") END_VERSIONS """ }