name: "srahumanscrubber_scrub"
description: Remove human reads from input FASTQs
keywords:
  - fastq
  - filter
  - human
tools:
  - "srahumanscrubber":
      description: "An SRA tool identifies and removes any significant human read, and outputs the edited (cleaned) fastq file for SRA submission."
      homepage: "https://github.com/ncbi/sra-human-scrubber"
      documentation: "https://github.com/ncbi/sra-human-scrubber"
      tool_dev_url: "https://github.com/ncbi/sra-human-scrubber"
      doi: "10.1186/s13059-021-02490-0"
      licence: "['Public Domain']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: FASTQ reads
      pattern: "*.fastq.gz"

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"
  - scrubbed_reads:
      type: file
      description: FASTQ file(s) scrubbed of human reads
      pattern: "*.{scrubbed.fastq.gz}"

authors:
  - "@rpetit3"
