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36 lines
1,018 B
Text
36 lines
1,018 B
Text
process GENMAP_MAPPABILITY {
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tag '$fasta'
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label 'process_high'
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conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' :
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'quay.io/biocontainers/genmap:1.3.0--h1b792b2_1' }"
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input:
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path index
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output:
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path "*.wig" , optional:true, emit: wig
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path "*.bedgraph" , optional:true, emit: bedgraph
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path "*.txt" , optional:true, emit: txt
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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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"""
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genmap \\
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map \\
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$args \\
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-I $index \\
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-O mappability
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
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END_VERSIONS
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"""
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}
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