name: "wfmash"
description: a pangenome-scale aligner
keywords:
  - long read alignment
  - pangenome-scale
  - all versus all
  - mashmap
  - wavefront
tools:
  - "wfmash":
      description: "a pangenome-scale aligner"
      homepage: https://github.com/waveygang/wfmash
      documentation: https://github.com/waveygang/wfmash
      tool_dev_url: https://github.com/waveygang/wfmash
      doi: 10.5281/zenodo.6949373
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta_gz:
      type: file
      description: BGZIPPED FASTA target file to create the mappings from.
      pattern: "{fa.gz,fna.gz,fasta.gz}"
  - paf:
      type: file
      description: Optional inpute file in PAF format to derive the precise alignments for.
      pattern: "*.{paf}"
  - query_self:
      type: boolean
      description: If set to true, the input FASTA will also be used as the query FASTA.
  - gzi:
      type: file
      description: The GZI index of the input FASTA file.
      pattern: "*.{gzi}"
  - fai:
      type: file
      description: The FASTA index of the input FASTA file.
      pattern: "*.{fai}"
  - fasta_query_list:
      type: file
      description: Optional inpute file in FASTA format specifying the query sequences as a list.
      pattern: "*.{fa,fna,fasta}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - paf:
      type: file
      description: Alignments in PAF format
      pattern: "*.{paf}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@subwaystation"
