process SAMTOOLS_VIEW { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::samtools=1.14" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' : 'quay.io/biocontainers/samtools:1.14--hb421002_0' }" input: tuple val(meta), path(input) path fasta output: tuple val(meta), path("*.bam") , emit: bam , optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta} -C" : "" def file_type = input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ view \\ --threads ${task.cpus-1} \\ ${reference} \\ $args \\ $input \\ $args2 \\ > ${prefix}.${file_type} cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }