process SEQTK_RENAME { 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(sequences) output: tuple val(meta), path("*.gz") , emit: sequences path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension = "fasta" if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) { extension = "fastq" } """ seqtk \\ rename \\ $args \\ $sequences \\ $prefix | \\ gzip -c --no-name > ${prefix}.renamed.${extension}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ }