process GATK4_FASTQTOSAM { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}" """ gatk FastqToSam \\ $read_files \\ -O ${prefix}.bam \\ -SM $prefix \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }