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45 lines
1.3 KiB
Text
45 lines
1.3 KiB
Text
process GLNEXUS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' :
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'quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0' }"
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input:
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tuple val(meta), path(gvcfs)
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output:
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tuple val(meta), path("*.bcf"), emit: bcf
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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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// Make list of GVCFs to merge
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def input = gvcfs.collect { it.toString() }
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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glnexus_cli \\
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--threads $task.cpus \\
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--mem-gbytes $avail_mem \\
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$args \\
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${input.join(' ')} \\
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> ${prefix}.bcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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