name: "metaphlan3_mergemetaphlantables"
description: Merges output abundance tables from MetaPhlAn3
keywords:
  - metagenomics
  - classification
  - merge
  - table
  - profiles
tools:
  - metaphlan3:
      description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
      homepage: https://huttenhower.sph.harvard.edu/metaphlan/
      documentation: https://github.com/biobakery/MetaPhlAn
      doi: "10.7554/eLife.65088"
      licence: ["MIT License"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - profiles:
      type: file
      description: List of per-sample MetaPhlAn3 taxonomic abundance tables
      pattern: "*"

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"
  - txt:
      type: txt
      description: Combined MetaPhlAn3 table
      pattern: "*.txt"

authors:
  - "@jfy133"