# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "bcl_demultiplex"
description: Demultiplex Illumina BCL data using bcl-convert or bcl2fastq
keywords:
  - bcl
  - bclconvert
  - bcl2fastq
  - demultiplex
  - fastq
modules:
  - bcl2fastq
  - bclconvert
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'string', lane: int ]
  - samplesheet:
      type: file
      description: |
        CSV file containing information about samples to be demultiplexed in Illumina SampleSheet format
  - flowcell:
      type: file
      description: Directory or tar archive containing Illumina BCL data, sequencer output directory
  - demultiplexer:
      type: string
      description: Which demultiplexer to use, bcl2fastq or bclconvert
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - fastq:
      type: file
      description: Demultiplexed fastq files
      pattern: "*.fastq.gz"
  - reports:
      type: file
      description: Demultiplexing reports
      pattern: "Reports/*"
  - interop:
      type: file
      description: InterOp files
      pattern: "InterOp/*"
  - stats:
      type: file
      description: Demultiplexing statistics (bcl2fastq only)
      pattern: "Stats/*"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@matthdsm"
