name: "bcl2fastq"
description: Demultiplex Illumina BCL files
keywords:
  - demultiplex
  - illumina
  - fastq
tools:
  - "bcl2fastq":
      description: "Demultiplex Illumina BCL files"
      homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software"
      documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf"
      licence: "ILLUMINA"

input:
  - meta:
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - samplesheet:
      type: file
      description: "Input samplesheet"
      pattern: "*.{csv}"
  - run_dir:
      type: directory
      description: "Input run directory containing RunInfo.xml and BCL data"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fastq:
      type: file
      description: Demultiplexed sample FASTQ files
      pattern: "**_S*_L00?_R?_00?.fastq.gz"
  - fastq_idx:
      type: file
      description: Optional demultiplexed index FASTQ files
      pattern: "**_S*_L00?_I?_00?.fastq.gz"
  - undetermined:
      type: file
      description: Optional undetermined sample FASTQ files
      pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz"
  - undetermined_idx:
      type: file
      description: Optional undetermined index FASTQ files
      pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz"
  - reports:
      type: file
      description: Demultiplexing Reports
      pattern: "Reports/*"
  - stats:
      type: file
      description: Statistics files
      pattern: "Stats/*"
  - interop:
      type: file
      description: Interop files
      pattern: "*.{bin}"
authors:
  - "@matthdsm"