process HIFIASM { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' : 'quay.io/biocontainers/hifiasm:0.15.4--h2e03b76_0' }" input: tuple val(meta), path(reads) path paternal_kmer_dump path maternal_kmer_dump val use_parental_kmers output: tuple val(meta), path("*.r_utg.gfa") , emit: raw_unitigs tuple val(meta), path("*.ec.bin") , emit: corrected_reads tuple val(meta), path("*.ovlp.source.bin") , emit: source_overlaps tuple val(meta), path("*.ovlp.reverse.bin"), emit: reverse_overlaps tuple val(meta), path("*.p_utg.gfa") , emit: processed_unitigs, optional: true tuple val(meta), path("*.asm.p_ctg.gfa") , emit: primary_contigs , optional: true tuple val(meta), path("*.asm.a_ctg.gfa") , emit: alternate_contigs, optional: true tuple val(meta), path("*.hap1.p_ctg.gfa") , emit: paternal_contigs , optional: true tuple val(meta), path("*.hap2.p_ctg.gfa") , emit: maternal_contigs , optional: true path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" if (use_parental_kmers) { """ hifiasm \\ $args \\ -o ${prefix}.asm \\ -t $task.cpus \\ -1 $paternal_kmer_dump \\ -2 $maternal_kmer_dump \\ $reads cat <<-END_VERSIONS > versions.yml "${task.process}": hifiasm: \$(hifiasm --version 2>&1) END_VERSIONS """ } else { // Phasing with Hi-C data is not supported yet """ hifiasm \\ $args \\ -o ${prefix}.asm \\ -t $task.cpus \\ $reads cat <<-END_VERSIONS > versions.yml "${task.process}": hifiasm: \$(hifiasm --version 2>&1) END_VERSIONS """ } }