name: "odgi_layout"
description: Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.
keywords:
  - variation graph
  - pangenome graph
  - gfa
  - graph layout
tools:
  - "odgi":
      description: "An optimized dynamic genome/graph implementation"
      homepage: "https://github.com/pangenome/odgi"
      documentation: "https://odgi.readthedocs.io/en/latest/"
      tool_dev_url: "https://github.com/pangenome/odgi"
      doi: "10.1093/bioinformatics/btac308"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - graph:
      type: file
      description: Pangenome graph in GFA v1.0 format or in ODGI binary format
      pattern: "*.{gfa,og}"

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"
  - lay:
      type: file
      description: File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified.
      pattern: "*.{lay}"
  - tsv:
      type: file
      description: File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified.
      pattern: "*.{tsv}"

authors:
  - "@subwaystation"
