name: sratools_fasterqdump
description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
keywords:
  - sequencing
  - FASTQ
  - dump
tools:
  - sratools:
      description: SRA Toolkit and SDK from NCBI
      homepage: https://github.com/ncbi/sra-tools
      documentation: https://github.com/ncbi/sra-tools/wiki
      tool_dev_url: https://github.com/ncbi/sra-tools
      licence: ["Public Domain"]

input:
  - meta:
      type: map
      description: >
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - sra:
      type: directory
      description: Directory containing ETL data for the given SRA.
      pattern: "*/*.sra"
  - ncbi_settings:
      type: file
      description: >
        An NCBI user settings file.
      pattern: "*.mkfg"

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"
  - reads:
      type: file
      description: Extracted FASTQ file or files if the sequencing reads are paired-end.
      pattern: "*.fastq.gz"

authors:
  - "@Midnighter"
