nf-core_modules/modules/deepvariant/main.nf
FriederikeHanssen c450b08a75
separate gvcf and vcf in output channels (#1371)
* separate gvcf and vcf in output channels

* regex not working, just using prefix now
2022-03-03 11:54:07 +01:00

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process DEEPVARIANT {
tag "$meta.id"
label 'process_medium'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the DeepVariant tool. Please use docker or singularity containers."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'google/deepvariant:1.3.0' :
'google/deepvariant:1.3.0' }"
input:
tuple val(meta), path(input), path(index), path(intervals)
path(fasta)
path(fai)
output:
tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf
tuple val(meta), path("${prefix}.g.vcf.gz"), emit: gvcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def regions = intervals ? "--regions ${intervals}" : ""
"""
/opt/deepvariant/bin/run_deepvariant \\
--ref=${fasta} \\
--reads=${input} \\
--output_vcf=${prefix}.vcf.gz \\
--output_gvcf=${prefix}.g.vcf.gz \\
${args} \\
${regions} \\
--num_shards=${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS
"""
}