name: "picard_fastqtosam"
description: Converts a FASTQ file to an unaligned BAM or SAM file.
keywords:
  - fastq
  - unaligned
  - bam
tools:
  - picard:
      description: |
        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
        data and formats such as SAM/BAM/CRAM and VCF.
      homepage: https://broadinstitute.github.io/picard/
      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard-
      tool_dev_url: https://github.com/broadinstitute/picard
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.

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"
  - bam:
      type: file
      description: Unaligned bam file
      pattern: "*.{bam}"

authors:
  - "@matthdsm"