mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
6243c3792c
* Add stubs for deepvariant [ci skip] * Update the stubs for deepvariant [ci skip] * functional with google docker image * cleanup * consume docker container within singularity executor * update the meta.yml file and ask for review * tweak the input channel shape and test data * tweak input data [ci skip] * update for the new syntax * remove the functions and rename meta vars * Update the arguments mechanism * update chr, region and checksum Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
43 lines
1.2 KiB
Text
43 lines
1.2 KiB
Text
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:1.2.0' :
|
|
'google/deepvariant:1.2.0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
path(fasta)
|
|
path(fai)
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz") , emit: vcf
|
|
tuple val(meta), path("*g.vcf.gz"), emit: gvcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
|
|
"""
|
|
/opt/deepvariant/bin/run_deepvariant \\
|
|
--ref=${fasta} \\
|
|
--reads=${bam} \\
|
|
--output_vcf=${prefix}.vcf.gz \\
|
|
--output_gvcf=${prefix}.g.vcf.gz \\
|
|
${args} \\
|
|
--num_shards=${task.cpus}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
|
|
END_VERSIONS
|
|
"""
|
|
|
|
}
|