name: "bases2fastq"
description: Demultiplex Element Biosciences bases files
keywords:
  - demultiplex
  - element
  - fastq
tools:
  - "bases2fastq":
      description: "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis"
      homepage: "https://go.elementbiosciences.com/bases2fastq-download"
      documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq"
      licence: "http://go.elembio.link/eula"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - run_manifest:
      type: file
      description: RunManifest file
      pattern: "*.{csv}"
  - run_dir:
      type: directory
      description: "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied"

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 sample FASTQ files
      pattern: "output/Samples/*/*_R*.fastq.gz"
  - sample_json:
      type: file
      description: Demultiplexed sample stats
      pattern: "output/Samples/*/*.json"
  - qc_report:
      type: file
      description: QC HTML report
      pattern: "output/*.html"
  - run_stats:
      type: file
      description: QC HTML report
      pattern: "output/*.html"
  - generated_run_manifest:
      type: file
      description: Updated Run Manifest JSON from the run_manifest csv
      pattern: "output/RunManifest.json"
  - metrics:
      type: file
      description: Sample metrics
      pattern: "output/Metrics.csv"
  - unassigned:
      type: file
      description: Unassigned Sequences
      pattern: "output/UnassignedSequences.csv"

authors:
  - "@Emiller88"