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9475960928
* fix a bug that the prefix is not handled by index. * build the test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BWA_INDEX {
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tag "$fasta"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7"
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} else {
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container "quay.io/biocontainers/bwa:0.7.17--hed695b0_7"
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}
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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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script:
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"""
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mkdir bwa
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bwa \\
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index \\
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$options.args \\
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-p bwa/${fasta.baseName} \\
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$fasta
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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