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https://github.com/MillironX/nf-core_modules.git
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54 lines
2.1 KiB
Text
54 lines
2.1 KiB
Text
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process SCRAMBLE_CLUSTERANALYSIS {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1':
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'quay.io/biocontainers/scramble:1.0.1--h779adbc_1' }"
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input:
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tuple val(meta), path(clusters)
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path fasta
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path mei_ref
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output:
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tuple val(meta), path("*_MEIs.txt") , optional:true, emit: meis_tab
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tuple val(meta), path("*_PredictedDeletions.txt") , optional:true, emit: dels_tab
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tuple val(meta), path("*.vcf") , optional:true, emit: vcf
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def blastdb = args.contains("--eval-dels") ? "makeblastdb -in ${fasta} -parse_seqids -title ${fasta} -dbtype nucl -out ${fasta}" : ""
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def reference = fasta ? "--ref `pwd`/${fasta}" : ""
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// The default file for the MEI reference is a file that's inside the container
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def mei_reference = mei_ref ? "`pwd`/${mei_ref}" : "/usr/local/share/scramble/resources/MEI_consensus_seqs.fa"
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def blastdb_version = args.contains("--eval-dels") ? "makeblastdb: \$(echo \$(makeblastdb -version 2>&1) | head -n 1 | sed 's/^makeblastdb: //; s/+ Package.*\$//')" : ""
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"""
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${blastdb}
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Rscript --vanilla /usr/local/share/scramble/bin/SCRAMble.R \\
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--install-dir /usr/local/share/scramble/bin \\
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${args} \\
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--cluster-file `pwd`/${clusters} \\
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${reference} \\
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--mei-refs ${mei_reference} \\
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--out-name `pwd`/${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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scramble: ${VERSION}
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${blastdb_version}
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END_VERSIONS
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"""
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}
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