process SNPSIFT_SPLIT { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::snpsift=4.3.1t" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpsift:4.3.1t--hdfd78af_3' : 'quay.io/biocontainers/snpsift:4.3.1t--hdfd78af_3' }" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.vcf"), emit: out_vcfs path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if (meta.split) { """ SnpSift \\ split \\ $args \\ $vcf cat <<-END_VERSIONS > versions.yml "${task.process}": snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' ) END_VERSIONS """ } else { """ SnpSift \\ split \\ -j \\ $args \\ $vcf \\ > ${prefix}.joined.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' ) END_VERSIONS """ } }