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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 {
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tag "$meta.id"
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label 'process_medium'
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used when using the DeepVariant tool. Please use docker or singularity containers."
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}
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'google/deepvariant:1.2.0' :
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'google/deepvariant:1.2.0' }"
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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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output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
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tuple val(meta), path("*g.vcf.gz"), emit: gvcf
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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/opt/deepvariant/bin/run_deepvariant \\
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--ref=${fasta} \\
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--reads=${bam} \\
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--output_vcf=${prefix}.vcf.gz \\
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--output_gvcf=${prefix}.g.vcf.gz \\
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${args} \\
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--num_shards=${task.cpus}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
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END_VERSIONS
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"""
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}
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