process MINIMAP2_ALIGN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null) container "${ 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(reads) path reference output: tuple val(meta), path("*.paf"), emit: paf path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" """ minimap2 \\ $args \\ -t $task.cpus \\ $reference \\ $input_reads \\ > ${prefix}.paf cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) END_VERSIONS """ }