process VCFANNO { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0': 'quay.io/biocontainers/vcfanno:0.3.3--h9ee0642_0' }" input: tuple val(meta), path(vcf), path(tbi) tuple val(meta), path(vcf_uncompressed) path toml path resource_dir output: tuple val(meta), path("*_annotated.vcf"), emit: vcf 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 input_vcf = vcf_uncompressed ?: vcf """ ln -sf $resource_dir/* \$(pwd) vcfanno \\ -p $task.cpus \\ $args \\ $toml \\ $input_vcf \\ > ${prefix}_annotated.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) END_VERSIONS """ }