name: seqwish_induce
description: Induce a variation graph in GFA format from alignments in PAF format
keywords:
  - induce
  - paf
  - gfa
  - graph
  - variation graph
tools:
  - seqwish:
      description: |
        seqwish implements a lossless conversion from pairwise alignments between
        sequences to a variation graph encoding the sequences and their alignments.
      homepage: https://github.com/ekg/seqwish
      documentation: https://github.com/ekg/seqwish
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - paf:
      type: file
      description: PAF file of alignments
      pattern: "*.{paf,paf.gz}"
  - fasta:
      type: file
      description: FASTA file used to generate alignments
      pattern: "*.{fa,fa.gz,fasta,fasta.gz}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gfa:
      type: file
      description: Variation graph in GFA 1.0 format
      pattern: "*.{gfa}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@heuermh"
