name: fgbio_fastqtobam
description: |
  Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
keywords:
  - fastqtobam
  - fgbio
tools:
  - fgbio:
      description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
      homepage: http://fulcrumgenomics.github.io/fgbio/
      documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
      tool_dev_url: https://github.com/fulcrumgenomics/fgbio
      doi: ""
      licence: ["MIT"]

input:
  - reads:
      type: file
      description: pair of reads to be converted into BAM file
      pattern: "*.{fastq.gz}"

  - read_structure:
      type: string
      description: |
        A read structure should always be provided for each of the fastq files.
        If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
        will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
        If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
        https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.yml}"
  - umibam:
      type: file
      description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
      pattern: "*.{bam}"

authors:
  - "@lescai"