process MINIMAP2_INDEX { label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' : 'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.mmi"), emit: index path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ minimap2 \\ -t $task.cpus \\ -d ${fasta.baseName}.mmi \\ $args \\ $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) END_VERSIONS """ }