process MACREL_CONTIGS { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::macrel=1.1.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macrel:1.1.0--py36hc5360cc_0': 'quay.io/biocontainers/macrel:1.1.0--py36hc5360cc_0' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*/*.smorfs.faa.gz") , emit: smorfs tuple val(meta), path("*/*.all_orfs.faa.gz") , emit: all_orfs tuple val(meta), path("*/*.prediction.gz") , emit: amp_prediction tuple val(meta), path("*/*.md") , emit: readme_file tuple val(meta), path("*/*_log.txt") , emit: log_file path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ macrel contigs \\ $args \\ --fasta $fasta \\ --output ${prefix}/ \\ --tag ${prefix} \\ --log-file ${prefix}/${prefix}_log.txt \\ --threads $task.cpus gzip --no-name ${prefix}/*.faa cat <<-END_VERSIONS > versions.yml "${task.process}": macrel: \$(echo \$(macrel --version | sed 's/macrel //g')) END_VERSIONS """ }