name: phyloflash
description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
keywords:
  - metagenomics
  - illumina datasets
  - phylogenetic composition
tools:
  - phyloflash:
      description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

      homepage: https://hrgv.github.io/phyloFlash/
      documentation: https://hrgv.github.io/phyloFlash/usage.html
      tool_dev_url: https://github.com/HRGV/phyloFlash
      doi: "10.1128/mSystems.00920-20"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: Channel containing single or paired-end reads
      pattern: "*.{fastq.gz,fq.gz}"
  - sliva_db:
      type: folder
      description: Folder containing the SILVA database
      pattern: "ref"
  - univec_db:
      type: folder
      description: Folder containing UniVec database
      pattern: "UniVec"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - results:
      type: folder
      description: Folder containing the results of phyloFlash analysis
      pattern: "${prefix}*"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@abhi18av"