process MINIMAP2_ALIGN { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' : 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }" input: tuple val(meta), path(reads) path reference val bam_format val cigar_paf_format val cigar_bam output: tuple val(meta), path("*.paf"), optional: true, emit: paf tuple val(meta), path("*.bam"), optional: true, emit: bam path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf" def cigar_paf = cigar_paf_format && !bam_format ? "-c" : '' def set_cigar_bam = cigar_bam && bam_format ? "-L" : '' """ minimap2 \\ $args \\ -t $task.cpus \\ $reference \\ $input_reads \\ $cigar_paf \\ $set_cigar_bam \\ $bam_output cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) END_VERSIONS """ }