name: sra_fastq
description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
keywords:
  - SRA
  - NCBI
  - sequencing
  - FASTQ
  - prefetch
  - fasterq-dump
modules:
  - custom/sratoolsncbisettings
  - sratools/prefetch
  - sratools/fasterqdump
input:
  - meta:
      type: map
      description: >
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - id:
      type: string
      description: >
        SRA run identifier.
# TODO Update when we decide on a standard for subworkflow docs
output:
  - meta:
      type: map
      description: >
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
      pattern: "*.fastq.gz"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@Midnighter"
