seqinspector/modules/nf-core/checkqc/meta.yml at ab6b2e1935de30d15f7910fe0be9fa6fc90115e1 · matrulda/seqinspector · GitHub

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name: "checkqc"
description: A simple program to parse Illumina NGS data and check it for
  quality criteria
keywords:
  - QC
  - Illumina
  - genomics
tools:
  - "checkqc":
      description: "A simple program to parse Illumina NGS data and check it for quality
        criteria."
      homepage: "https://github.com/Molmed/checkQC"
      documentation: "http://checkqc.readthedocs.io/en/latest/"
      doi: "10.21105/joss.00556"
      licence:
        - "GPL v3"
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - run_dir:
        type: file
        description: |
          Illumina sequencing run directory
          Can be directory or a compressed tar (tar.gz) of the directory
        ontologies: []
  - checkqc_config:
      type: file
      description: CheckQC configuration file
      pattern: "*.{yml,yaml}"
      ontologies:
        - edam: http://edamontology.org/format_3750
output:
  report:
    - - meta:
          type: file
          description: CheckQC report in json format
          pattern: "*checkqc_report.json"
          ontologies:
            - edam: http://edamontology.org/format_3464
      - "*checkqc_report.json":
          type: file
          description: CheckQC report in json format
          pattern: "*checkqc_report.json"
          ontologies:
            - edam: http://edamontology.org/format_3464
  versions_checkqc:
    - - ${task.process}:
          type: string
          description: The name of the process
      - checkqc:
          type: string
          description: The name of the tool
      - 'checkqc --version | sed -e "s/checkqc, version //g"':
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - checkqc:
          type: string
          description: The name of the tool
      - 'checkqc --version | sed -e "s/checkqc, version //g"':
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@matrulda"