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35 lines
997 B
Text
35 lines
997 B
Text
process DSHBIO_EXPORTSEGMENTS {
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tag "${meta.id}"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::dsh-bio=2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/dsh-bio:2.1--hdfd78af_0' :
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'quay.io/biocontainers/dsh-bio:2.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(gfa)
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output:
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tuple val(meta), path("*.fa.gz"), emit: fasta
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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 ?: "${meta.id}"
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"""
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dsh-bio \\
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export-segments \\
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$args \\
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-i $gfa \\
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-o ${prefix}.fa.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dshbio: \$(dsh-bio --version 2>&1 | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ')
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END_VERSIONS
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"""
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}
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