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* Add atlas/splitmerge module * Finish the tests for atlas/splitmerge * Prettier * Update modules/atlas/splitmerge/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Remove curly brackets from meta.yml parameters For single-file outputs, as reviewed * Lintung: Remove trailing white-space Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
36 lines
1.1 KiB
Text
36 lines
1.1 KiB
Text
process ATLAS_SPLITMERGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::atlas=0.9.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/atlas:0.9.9--h082e891_0':
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'quay.io/biocontainers/atlas:0.9.9--h082e891_0' }"
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input:
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tuple val(meta), path(bam), path(bai), path(read_group_settings), path(blacklist)
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output:
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tuple val(meta), path("*_mergedReads.bam"), path("*.txt.gz"), emit: data
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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 optional = blacklist ? 'blacklist=${blacklist}' : ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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atlas \\
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task=splitMerge bam=${bam} \\
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readGroupSettings=${read_group_settings}\\
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$optional \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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atlas: \$((atlas 2>&1) | grep Atlas | head -n 1 | sed -e 's/^[ \t]*Atlas //')
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END_VERSIONS
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"""
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}
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