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https://github.com/MillironX/nf-core_modules.git
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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
45 lines
1.3 KiB
Text
45 lines
1.3 KiB
Text
process TABIX_BGZIPTABIX {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
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'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
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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 args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz
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tabix $args2 ${prefix}.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.gz
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touch ${prefix}.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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