process FALCO { tag "$meta.id" label 'process_single' conda (params.enable_conda ? "bioconda::falco=1.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/falco:1.2.1--h867801b_3': 'quay.io/biocontainers/falco:1.2.1--h867801b_3' }" input: tuple val(meta), path(reads) output: tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.txt") , emit: txt 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 ( reads.toList().size() == 1 ) { """ falco $args --threads $task.cpus ${reads} -D ${prefix}_data.txt -S ${prefix}_summary.txt -R ${prefix}_report.html cat <<-END_VERSIONS > versions.yml "${task.process}": falco:\$( falco --version | sed -e "s/falco//g" ) END_VERSIONS """ } else { """ falco $args --threads $task.cpus ${reads} cat <<-END_VERSIONS > versions.yml "${task.process}": falco:\$( falco --version | sed -e "s/falco//g" ) END_VERSIONS """ } stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_data.txt touch ${prefix}_fastqc_data.html touch ${prefix}_summary.txt cat <<-END_VERSIONS > versions.yml "${task.process}": falco: \$( falco --version | sed -e "s/falco v//g" ) END_VERSIONS """ }