process SEQTK_SAMPLE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" input: tuple val(meta), path(reads) val sample_size output: tuple val(meta), path("*.fastq.gz"), emit: reads path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if (meta.single_end) { """ seqtk \\ sample \\ $args \\ $reads \\ $sample_size \\ | gzip --no-name > ${prefix}.fastq.gz \\ cat <<-END_VERSIONS > versions.yml "${task.process}": seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } else { if (!(args ==~ /.*-s[0-9]+.*/)) { args += " -s100" } """ seqtk \\ sample \\ $args \\ ${reads[0]} \\ $sample_size \\ | gzip --no-name > ${prefix}_1.fastq.gz \\ seqtk \\ sample \\ $args \\ ${reads[1]} \\ $sample_size \\ | gzip --no-name > ${prefix}_2.fastq.gz \\ cat <<-END_VERSIONS > versions.yml "${task.process}": seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } }