name: gfaffix
description: Collapse walk-preserving shared affixes in variation graphs in GFA format
keywords:
  - gfa
  - graph
  - pangenome
  - variation graph
tools:
  - gfaffix:
      description: |
        GFAffix identifies walk-preserving shared affixes in variation graphs and
        collapses them into a non-redundant graph structure.
      homepage: https://github.com/marschall-lab/GFAffix
      documentation: https://github.com/marschall-lab/GFAffix
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gfa:
      type: file
      description: Variation graph in GFA format
      pattern: "*.{gfa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gfa:
      type: file
      description: Non-redundant variation graph in GFA 1.0 format
      pattern: "*.{gfa}"
  - affixes:
      type: file
      description: Shared affixes in tab-separated values (TSV) text format
      pattern: "*.{txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@heuermh"