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42 lines
1.6 KiB
Text
42 lines
1.6 KiB
Text
process LAST_MAFCONVERT {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? 'bioconda::last=1250' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
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'quay.io/biocontainers/last:1250--h2e03b76_0' }"
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input:
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tuple val(meta), path(maf)
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val(format)
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output:
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tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
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tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
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tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
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tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
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tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
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tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
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tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
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tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
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tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
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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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maf-convert $args $format $maf | gzip --no-name \\
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> ${prefix}.${format}.gz
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# maf-convert has no --version option but lastdb (part of the same package) has.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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last: \$(lastdb --version 2>&1 | sed 's/lastdb //')
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END_VERSIONS
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"""
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}
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