process BWAMEM2_INDEX { tag "$fasta" label 'process_high' conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : 'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" input: path fasta output: path "bwamem2" , emit: index path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' """ mkdir bwamem2 bwa-mem2 \\ index \\ $args \\ $fasta -p bwamem2/${fasta} cat <<-END_VERSIONS > versions.yml "${task.process}": bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') END_VERSIONS """ }