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f079367416
* Building Picard liftovervcf module * Building Picard liftovervcf module_test * Building Picard liftovervcf pytest * Module for picard liftover vcf created * Fixed files after linting test * Fixed trailing whitespace * Checked files with prettier * further formatting with prettier * Fixed test.yml * Fixed input variable names * Changed contain test.liftef.vcf * Changed contain in test.yml test.liftef.vcf * Run prittier * Going back to previous version of test.yml * downgrading picard to 2.26.10 from 2.26.11 * Update modules/picard/liftovervcf/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Print available memory Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Output from .vcf to .vcf.gz * Added spaces to align emit * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Removing md5sum test Co-authored-by: jemten <jemten@users.noreply.github.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
49 lines
1.5 KiB
Text
49 lines
1.5 KiB
Text
process PICARD_LIFTOVERVCF {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
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input:
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tuple val(meta), path(input_vcf)
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path dict
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path chain
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path fasta
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output:
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tuple val(meta), path("*lifted.vcf.gz") , emit: vcf_lifted
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tuple val(meta), path("*unlifted.vcf.gz"), emit: vcf_unlifted
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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 ?: "${meta.id}"
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def avail_mem = 1
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if (!task.memory) {
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log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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LiftoverVcf \\
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$args \\
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I=$input_vcf \\
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O=${prefix}.lifted.vcf.gz \\
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CHAIN=$chain \\
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REJECT=${prefix}.unlifted.vcf.gz \\
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R=$fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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