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b6fe5d2643
* add atlas/pmd * update atlas/pmd tests * Add atlas/PMD module * Remove comment * Run Prettier * Incorporate Review by @jfy133 Co-authored-by: maxibor <maxime.borry@gmail.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process ATLAS_PMD {
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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(pool_rg_txt)
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path(fasta)
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path(fai)
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output:
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tuple val(meta), path("*_PMD_input_Empiric.txt") , emit: empiric
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tuple val(meta), path("*_PMD_input_Exponential.txt"), emit: exponential
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tuple val(meta), path("*_PMD_Table_counts.txt") , emit: counts
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tuple val(meta), path("*_PMD_Table.txt") , emit: table
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def pool_rg_txt = pool_rg_txt ? "poolReadGroups=${pool_rg_txt}" : ""
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"""
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atlas \\
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$pool_rg_txt \\
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task=PMD \\
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bam=${bam} \\
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fasta=${fasta} \\
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$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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