---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "sumtaxonomy"
description: Small module to summarise taxonomy tables
keywords:
  - taxonomy
  - summarise
tools:
  - "sumtaxonomy":
      description: "R script that summarises taxonomy tables"

input:
  # Only when we have meta
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - db:
        type: string
        description: Name of database, e.g. gtdb
    - taxonomy:
        type: file
        description: Taxonomy in tsv format
        pattern: "*.tsv(.gz)?"

  - - feature_counts:
        type: file
        description: File with gene counts

  - - taxname:
        type: string
        description: Name of taxonomy, e.g. eukulele

output:
  - taxonomy_summary:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*_summary.tsv.gz":
          type: file
          pattern: "*._summary.tsv.gz"

  - versions:
      - "versions.yml":
          type: file
          description: File containing software versions
          pattern: "versions.yml"

authors:
  - "@erikrikarddaniel"
maintainers:
  - "@erikrikarddaniel"
