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https://github.com/MillironX/nf-core_modules.git
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be8d7b3293
* Rollback version * Start work rollback to 0.4.1 * Further changes * Re do dynamic flag creation * Prettier.
69 lines
2 KiB
Text
69 lines
2 KiB
Text
process MALT_BUILD {
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label 'process_high'
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conda (params.enable_conda ? "bioconda::malt=0.41" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
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'quay.io/biocontainers/malt:0.41--1' }"
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input:
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path fastas
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val seq_type
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path mapping_file
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val mapping_type
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val mapping_db
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output:
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path "malt_index/" , emit: index
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path "versions.yml" , emit: versions
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path "malt-build.log", emit: log
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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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def avail_mem = 6
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if (!task.memory) {
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log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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def valid_db = ['eggnog', 'interpro2go', 'kegg', 'seed', 'taxonomy']
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if ( !valid_db.contains(mapping_db) ) { error "Unrecognised mapping database value for MALT_BUILD. Options: eggnog, interpro2go, kegg, seed, taxonomy" }
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switch ( "${mapping_type}" ) {
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case "gi":
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mapping_prefix = "-g"; break
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case "ref":
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if ( mapping_db == "taxonomy" ) {
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mapping_prefix = '-a'
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} else {
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mapping_prefix = "-r"
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};break
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case "syn":
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mapping_prefix = "-s"; break
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default:
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error '[MALT_BUILD] Mapping type not recognised. Options: gi, ref, syn'; break
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}
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type_flag = mapping_prefix + '2' + mapping_db + " " + mapping_file
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"""
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malt-build \\
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-v \\
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--input ${fastas.join(' ')} \\
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-s $seq_type \\
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-d 'malt_index/' \\
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-t $task.cpus \\
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$args \\
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$type_flag |&tee malt-build.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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malt: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2)
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END_VERSIONS
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"""
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}
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