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37 lines
975 B
Text
37 lines
975 B
Text
process BEDTOOLS_GETFASTA {
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tag "$bed"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
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'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
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input:
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path bed
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path fasta
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output:
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path "*.fa" , 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 ?: "${bed.baseName}"
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"""
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bedtools \\
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getfasta \\
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$args \\
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-fi $fasta \\
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-bed $bed \\
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-fo ${prefix}.fa
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
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END_VERSIONS
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"""
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}
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