process FARGENE { tag "$meta.id" label 'process_low' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::fargene=0.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' : 'quay.io/biocontainers/fargene:0.1--py27h21c881e_4' }" input: // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag tuple val(meta), path(input) val hmm_model output: tuple val(meta), path("*.log") , emit: log tuple val(meta), path("${prefix}/results_summary.txt") , emit: txt tuple val(meta), path("${prefix}/hmmsearchresults/*.out") , optional: true, emit: hmm tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs.fasta") , optional: true, emit: orfs tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs-amino.fasta") , optional: true, emit: orfs_amino tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs.fasta") , optional: true, emit: contigs tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs-peptides.fasta") , optional: true, emit: contigs_pept tuple val(meta), path("${prefix}/predictedGenes/*filtered.fasta") , optional: true, emit: filtered tuple val(meta), path("${prefix}/predictedGenes/*filtered-peptides.fasta") , optional: true, emit: filtered_pept tuple val(meta), path("${prefix}/retrievedFragments/all_retrieved_*.fastq") , optional: true, emit: fragments tuple val(meta), path("${prefix}/retrievedFragments/retrievedFragments/trimmedReads/*.fasta"), optional: true, emit: trimmed tuple val(meta), path("${prefix}/spades_assembly/*") , optional: true, emit: spades tuple val(meta), path("${prefix}/tmpdir/*.fasta") , optional: true, emit: metagenome tuple val(meta), path("${prefix}/tmpdir/*.out") , optional: true, emit: tmp path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ fargene \\ $args \\ -p $task.cpus \\ -i $input \\ --hmm-model $hmm_model \\ -o $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": fargene: $VERSION END_VERSIONS """ }