name: "centrifuge_kreport"
description: Creates Kraken-style reports from centrifuge out files
keywords:
  - metagenomics
tools:
  - centrifuge:
      description: Centrifuge is a classifier for metagenomic sequences.
      homepage: https://ccb.jhu.edu/software/centrifuge/
      documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
      doi: 10.1101/gr.210641.116
      licence: ["GPL v3"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: File containing the centrifuge classification report
      pattern: "*.{txt}"

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"
  - kreport:
      type: file
      description: |
        File containing kraken-style report from centrifuge
        out files.
      pattern: "*.{txt}"
authors:
  - "@sofstam"
  - "@jfy133"