name: smoothxg
description: Linearize and simplify variation graph in GFA format using blocked partial order alignment
keywords:
  - gfa
  - graph
  - pangenome
  - variation graph
  - POA
tools:
  - smoothxg:
      description: |
        smoothxg linearizes and simplifies variation graphs using blocked partial
        order alignment.
      homepage: https://github.com/pangenome/smoothxg
      documentation: https://github.com/pangenome/smoothxg
      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 1.0 format
      pattern: "*.{gfa}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gfa:
      type: file
      description: Linearized and simplified graph in GFA 1.0 format
      pattern: "*.smoothxg.{gfa}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - maf:
      type: file
      description: write the multiple sequence alignments (MSAs) in MAF format in this file (optional)
      pattern: "*.{maf}"
authors:
  - "@heuermh, @subwaystation"
