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b3acfc54f5
* Support non-GFF input * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Fix linting error Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
69 lines
3.5 KiB
Text
69 lines
3.5 KiB
Text
process ANTISMASH_ANTISMASHLITE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
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'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
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containerOptions {
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workflow.containerEngine == 'singularity' ?
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"-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
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workflow.containerEngine == 'docker' ?
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"-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
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''
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}
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input:
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tuple val(meta), path(sequence_input)
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path(databases)
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path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
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path(gff)
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output:
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tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
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tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files
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tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
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tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
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tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
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tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
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tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
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tuple val(meta), path("${prefix}/*.json") , emit: json_results
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tuple val(meta), path("${prefix}/*.log") , emit: log
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tuple val(meta), path("${prefix}/*.zip") , emit: zip
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tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
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tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
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tuple val(meta), path("${prefix}/index.html") , emit: html
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tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
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tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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gff_flag = gff ? "--genefinding-gff3 ${gff}" : ""
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"""
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## We specifically do not include on-the-fly annotations (--genefinding-tool none) as
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## this should be run as a separate module for versioning purposes
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antismash \\
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$args \\
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$gff_flag \\
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-c $task.cpus \\
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--output-dir $prefix \\
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--genefinding-tool none \\
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--logfile $prefix/${prefix}.log \\
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--databases $databases \\
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$sequence_input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
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END_VERSIONS
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"""
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}
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