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https://github.com/MillironX/nf-core_modules.git
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a25423dbb9
* add gatk4/combinegvcfs module * update gatk4/combinegvcfs * loop to create a string adding -V to each vcf file * add contains for variable md5 * rm whitespace * meta in output * fix indentations * fix indentations * move tmpdir to args and update conda version Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
47 lines
1.5 KiB
Text
47 lines
1.5 KiB
Text
process GATK4_COMBINEGVCFS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf), path(vcf_idx)
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path (fasta)
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path (fasta_fai)
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path (fasta_dict)
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output:
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tuple val(meta), path("*.combined.g.vcf.gz"), emit: combined_gvcf
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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 avail_mem = 3
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if (!task.memory) {
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log.info '[GATK COMBINEGVCFS] 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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def input_files = vcf.collect{"-V ${it}"}.join(' ') // add '-V' to each vcf file
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"""
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gatk \\
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--java-options "-Xmx${avail_mem}g" \\
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CombineGVCFs \\
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-R ${fasta} \\
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-O ${prefix}.combined.g.vcf.gz \\
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${args} \\
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${input_files}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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