name: "fqtk"
description: Demultiplex fastq files
keywords:
  - demultiplex
  - fastq
  - rust
tools:
  - "fqtk":
      description: "A toolkit for working with FASTQ files, written in Rust."
      homepage: "https://github.com/fulcrumgenomics/fqtk"
      documentation: "https://github.com/fulcrumgenomics/fqtk"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - sample_sheet:
      type: file
      description: Tsv file, with two columns sample_id and barcode
      pattern: "*.{tsv}"
  - fastq_readstructure_pairs:
      type: map
      description: List of lists i.e. [[<fastq file name>, <read structure>, <absolute path to fastq directory>],...]

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"
  - sample_fastq:
      type: file
      description: Demultiplexed per-sample FASTQ files
      pattern: "output/*R*.fastq.gz"
  - metrics:
      type: file
      description: |
        Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best
      pattern: "output/demux-metrics.txt"
  - most_frequent_unmatched:
      type: file
      description: |
        File containing unmatched fastq records
      pattern: "output/unmatched*.fq.gz"

authors:
  - "Samantha White @sam-white04"
