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1f8f86b793
* takes gunzip out of fargene main.nf * update definition of input * options.args -> args Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
50 lines
2.9 KiB
Text
50 lines
2.9 KiB
Text
def VERSION = '0.1' // Version information not provided by tool on CLI
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process FARGENE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::fargene=0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' :
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'quay.io/biocontainers/fargene:0.1--py27h21c881e_4' }"
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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("${prefix}/tmpdir/*.out") , optional: true, emit: tmp
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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"""
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fargene \\
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$args \\
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-p $task.cpus \\
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-i $input \\
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--hmm-model $hmm_model \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fargene: $VERSION
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END_VERSIONS
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"""
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}
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