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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process ABACAS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' :
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'quay.io/biocontainers/abacas:1.3.1--pl526_0' }"
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input:
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tuple val(meta), path(scaffold)
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path fasta
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output:
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tuple val(meta), path('*.abacas*'), emit: results
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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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"""
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abacas.pl \\
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-r $fasta \\
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-q $scaffold \\
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$args \\
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-o ${prefix}.abacas
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mv nucmer.delta ${prefix}.abacas.nucmer.delta
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mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
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mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
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mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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abacas: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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