name: metaphlan3_metaphlan3
description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
keywords:
  - metagenomics
  - classification
  - fastq
  - bam
  - fasta
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 ]
  - input:
      type: file
      description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
      pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
  - metaphlan_db:
      type: file
      description: |
        Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
        Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!
      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"
  - profile:
      type: file
      description: Tab-separated output file of the predicted taxon relative abundances
      pattern: "*.{txt}"
  - biom:
      type: file
      description: General-use format for representing biological sample by observation contingency tables
      pattern: "*.{biom}"
  - bowtie2out:
      type: file
      description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )
      pattern: "*.{bowtie2out.txt}"

authors:
  - "@MGordon09"