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53 lines
1.6 KiB
Text
53 lines
1.6 KiB
Text
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process ATLAS_CALL {
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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)
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path fasta
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path fai
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path recal
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path pmd
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path known_alleles
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val method
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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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 ?: "${meta.id}"
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def recal_file = recal ? "recal=${recal}" : ""
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def pmd_file = pmd ? "pmdFile=${pmd}" : ""
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def known_alleles_file = known_alleles ? "pmdFile=${known_alleles}" : ""
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def valid_method = ['MLE', 'Bayesian', 'allelePresence', 'randomBase', 'majorityBase']
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if ( !valid_method.contains(method) ) { error "Unrecognised calling method for ATLAS_CALL. Options: MLE, Bayesian, allelePresence, randomBase, majorityBase" }
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"""
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atlas \\
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task=call \\
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bam=${bam} \\
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fasta=${fasta} \\
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$recal_file \\
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$pmd_file \\
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method=${method} \\
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$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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