name: miniasm
description: A very fast OLC-based de novo assembler for noisy long reads
keywords:
  - assembly
  - pacbio
  - nanopore
tools:
  - miniasm:
      description: Ultrafast de novo assembly for long noisy reads (though having no consensus step)
      homepage: https://github.com/lh3/miniasm
      documentation: https://github.com/lh3/miniasm
      tool_dev_url: https://github.com/lh3/miniasm
      doi: "10.1093/bioinformatics/btw152"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: List of input PacBio/ONT FastQ files.
      pattern: "*.{fastq,fastq.gz,fq,fq.gz}"
  - paf:
      type: file
      description: Alignment in PAF format
      pattern: "*{.paf,.paf.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - gfa:
      type: file
      description: Assembly graph
      pattern: "*.gfa.gz"
  - assembly:
      type: file
      description: Genome assembly
      pattern: "*.fasta.gz"

authors:
  - "@avantonder"