process FILTLONG { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : 'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }" input: tuple val(meta), path(shortreads), path(longreads) output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), 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}" def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!" """ filtlong \\ $short_reads \\ $args \\ $longreads \\ 2> ${prefix}.log \\ | gzip -n > ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" ) END_VERSIONS """ }