name: samtools_fastq
description: Converts a SAM/BAM/CRAM file to FASTQ
keywords:
  - bam
  - sam
  - cram
  - fastq
tools:
  - samtools:
      description: |
        SAMtools is a set of utilities for interacting with and post-processing
        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
        These files are generated as output by short read aligners like BWA.
      homepage: http://www.htslib.org/
      documentation: http://www.htslib.org/doc/samtools.html
      doi: 10.1093/bioinformatics/btp352
      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}"
  - interleave:
      type: boolean
      description: Set true for interleaved fastq file

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"
  - fastq:
      type: file
      description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
      pattern: "*_{1,2}.fastq.gz"
  - interleaved:
      type: file
      description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
      pattern: "*_interleaved.fastq.gz"
  - singleton:
      type: file
      description: Compressed FASTQ file with singleton reads
      pattern: "*_singleton.fastq.gz"
  - other:
      type: file
      description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
      pattern: "*_other.fastq.gz"

authors:
  - "@priyanka-surana"
  - "@suzannejin"