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c9dc0a82d0
* commit 08/07 * fixed formatting * atlas recal commit - corrected formatting * Fix tests * Fix meta.yml * Prettier * Delete nextflow * yaml > yml * Delete meta.yaml * Fix test * Forgot to run prettier? Co-authored-by: ltcrod <luca_traverso@kickseed.localdomain> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
46 lines
1.4 KiB
Text
46 lines
1.4 KiB
Text
process ATLAS_RECAL {
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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(empiric), path(readgroups)
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path(alleles)
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path(invariant_sites)
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output:
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tuple val(meta), path("*.txt"), emit:recal_patterns
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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 ?: "${meta.id}"
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def PMD = empiric ? "pmdFile=${empiric}" : ""
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def ALLELES = alleles ? "alleleFile=${alleles}" : ""
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def INVARIANTS = invariant_sites ? "window=${invariant_sites}" : ""
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def READGROUPS = readgroups ? "poolReadGroups=${readgroups}" : ""
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"""
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atlas \\
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task=recal \\
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bam=$bam \\
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$PMD \\
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$READGROUPS \\
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$ALLELES \\
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$INVARIANTS \\
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out=$prefix \\
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$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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