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64 lines
3.4 KiB
Text
64 lines
3.4 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '0.1'
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process FARGENE {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::fargene=0.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4"
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} else {
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container "quay.io/biocontainers/fargene:0.1--py27h21c881e_4"
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}
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input:
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// input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag
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tuple val(meta), path(input)
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val hmm_model
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output:
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path "*.log" , emit: log
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path "${prefix}/results_summary.txt" , emit: txt
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tuple val(meta), path("${prefix}/hmmsearchresults/*.out") , optional: true, emit: hmm
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tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs.fasta") , optional: true, emit: orfs
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tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs-amino.fasta") , optional: true, emit: orfs_amino
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tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs.fasta") , optional: true, emit: contigs
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tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs-peptides.fasta") , optional: true, emit: contigs_pept
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tuple val(meta), path("${prefix}/predictedGenes/*filtered.fasta") , optional: true, emit: filtered
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tuple val(meta), path("${prefix}/predictedGenes/*filtered-peptides.fasta") , optional: true, emit: filtered_pept
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tuple val(meta), path("${prefix}/retrievedFragments/all_retrieved_*.fastq") , optional: true, emit: fragments
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tuple val(meta), path("${prefix}/retrievedFragments/retrievedFragments/trimmedReads/*.fasta"), optional: true, emit: trimmed
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tuple val(meta), path("${prefix}/spades_assembly/*") , optional: true, emit: spades
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tuple val(meta), path("${prefix}/tmpdir/*.fasta") , optional: true, emit: metagenome
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tuple val(meta), path("${prefix}/tmpdir/*.out") , optional: true, emit: tmp
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path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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gzip \\
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-cdf $input \\
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> unziped.fa |
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fargene \\
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$options.args \\
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-p $task.cpus \\
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-i unziped.fa \\
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--hmm-model $hmm_model \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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END_VERSIONS
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"""
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}
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