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49b18b1639
* add stub section * add stub for bcftools norm * add stub to more modules * fix expansionhunter tests * revert changes -picard * Update stub to write version no.s to a file * add picard * revert picard again * add stubs to more modules * fix bwamem2 * add bcftools view * add stubs * fix svdb query * review suggestions
49 lines
1.2 KiB
Text
49 lines
1.2 KiB
Text
process BWAMEM2_INDEX {
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tag "$fasta"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' :
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'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }"
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input:
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path fasta
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output:
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path "bwamem2" , 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 bwamem2
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bwa-mem2 \\
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index \\
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$args \\
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$fasta -p bwamem2/${fasta}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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END_VERSIONS
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"""
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stub:
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"""
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mkdir bwamem2
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touch bwamem2/${fasta}.0123
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touch bwamem2/${fasta}.ann
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touch bwamem2/${fasta}.pac
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touch bwamem2/${fasta}.amb
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touch bwamem2/${fasta}.bwt.2bit.64
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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END_VERSIONS
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"""
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}
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