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 """ }