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33 lines
869 B
Text
33 lines
869 B
Text
process GFFREAD {
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tag "$gff"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' :
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'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }"
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input:
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path gff
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output:
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path "*.gtf" , emit: gtf
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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 ?: "${gff.baseName}"
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"""
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gffread \\
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$gff \\
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$args \\
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-o ${prefix}.gtf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gffread: \$(gffread --version 2>&1)
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END_VERSIONS
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"""
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}
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