process NANOLYSE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' : 'quay.io/biocontainers/nanolyse:1.2.0--py_0' }" input: tuple val(meta), path(fastq) path fasta output: tuple val(meta), path("*.fastq.gz"), emit: fastq path "*.log" , emit: log 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}" """ gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz mv NanoLyse.log ${prefix}.nanolyse.log cat <<-END_VERSIONS > versions.yml "${task.process}": nanolyse: \$(NanoLyse --version 2>&1 | sed -e "s/NanoLyse //g") END_VERSIONS """ }