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35 lines
878 B
Text
35 lines
878 B
Text
process BWA_INDEX {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' :
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'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }"
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input:
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path fasta
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output:
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path "bwa" , emit: index
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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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mkdir bwa
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bwa \\
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index \\
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$args \\
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-p bwa/${fasta.baseName} \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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END_VERSIONS
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"""
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}
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