nf-core_modules/modules/picard/liftovervcf/main.nf

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process PICARD_LIFTOVERVCF {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(input_vcf)
path dict
path chain
path fasta
output:
tuple val(meta), path("*lifted.vcf.gz") , emit: vcf_lifted
tuple val(meta), path("*unlifted.vcf.gz"), emit: vcf_unlifted
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 1
if (!task.memory) {
log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
LiftoverVcf \\
$args \\
--INPUT $input_vcf \\
--OUTPUT ${prefix}.lifted.vcf.gz \\
--CHAIN $chain \\
--REJECT ${prefix}.unlifted.vcf.gz \\
--REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
}