name: samtools_collatefastq
description: |
  The module uses collate and then fastq methods from samtools to
  convert a SAM, BAM or CRAM file to FASTQ format
keywords:
  - bam2fq
  - samtools
  - fastq
tools:
  - samtools:
      description: Tools for dealing with SAM, BAM and CRAM files
      homepage: None
      documentation: http://www.htslib.org/doc/1.1/samtools.html
      tool_dev_url: None
      doi: ""
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
        or a single interleaved .fq.gz file if the user chooses not to split the reads.
      pattern: "*.fq.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@lescai"
  - "@maxulysse"