name: hifiasm
description: Whole-genome assembly using PacBio HiFi reads
keywords:
  - genome assembly
  - haplotype resolution
  - phasing
  - PacBio
  - HiFi
  - long reads
tools:
  - hifiasm:
      description: Haplotype-resolved assembler for accurate HiFi reads
      homepage: https://github.com/chhylp123/hifiasm
      documentation: https://github.com/chhylp123/hifiasm
      tool_dev_url: https://github.com/chhylp123/hifiasm
      doi: "10.1038/s41592-020-01056-5"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: FASTQ file with PacBio HiFi reads
      pattern: "*.{fastq}"
  - paternal_kmer_dump:
      type: file
      description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
  - maternal_kmer_dump:
      type: file
      description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
  - use_parental_kmers:
      type: logical
      description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - raw_unitigs:
      type: file
      description: Raw unitigs
      pattern: "*.r_utg.gfa"
  - processed_unitigs:
      type: file
      description: Processed unitigs
      pattern: "*.p_utg.gfa"
  - primary_contigs:
      type: file
      description: Primary contigs
      pattern: "*.asm.p_ctg.gfa"
  - alternate_contigs:
      type: file
      description: Alternative contigs
      pattern: "*.asm.a_ctg.gfa"
  - paternal_contigs:
      type: file
      description: Paternal contigs
      pattern: "*.hap1.p_ctg.gfa"
  - maternal_contigs:
      type: file
      description: Maternal contigs
      pattern: "*.hap2.p_ctg.gfa"
  - corrected_reads:
      type: file
      description: Corrected reads
      pattern: "*.ec.bin"
  - source_overlaps:
      type: file
      description: Source overlaps
      pattern: "*.ovlp.source.bin"
  - reverse_overlaps:
      type: file
      description: Reverse overlaps
      pattern: "*.ovlp.reverse.bin"

authors:
  - "@sidorov-si"