name: centrifuge_centrifuge
description: Classifies metagenomic sequence data
keywords:
  - classify
  - metagenomics
  - fastq
  - db
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 ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - db:
      type: directory
      description: Path to directory containing centrifuge database files
  - save_unaligned:
      type: boolean
      description: If true unmapped fastq files are saved
  - save_aligned:
      type: boolean
      description: If true mapped fastq files are saved
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: |
        File containing a classification summary
      pattern: "*.{report.txt}"
  - results:
      type: file
      description: |
        File containing classification results
      pattern: "*.{results.txt}"
  - sam:
      type: file
      description: |
        Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
      pattern: "*.{sam,tab}"
  - fastq_unmapped:
      type: file
      description: Unmapped fastq files
      pattern: "*.unmapped.fastq.gz"
  - fastq_mapped:
      type: file
      description: Mapped fastq files
      pattern: "*.mapped.fastq.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@sofstam"
  - "@jfy133"
  - "@sateeshperi"
maintainers:
  - "@sofstam"
  - "@jfy133"
  - "@sateeshperi"
