seqinspector/modules/nf-core/multiqcsav/meta.yml at 9074b7afd70c6a910db23bced1185d64659eea3e · nkongenelly/seqinspector · GitHub

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name: multiqcsav
description: Aggregate results from bioinformatics analyses across many samples
  into a single report, with support for multiqc_sav plugin
keywords:
  - QC
  - bioinformatics tools
  - Beautiful stand-alone HTML report
  - Illumina
  - Sequencing Analysis Viewer
  - SAV
tools:
  - multiqc:
      description: |
        MultiQC searches a given directory for analysis logs and compiles a HTML report.
        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
      homepage: https://multiqc.info/
      documentation: https://multiqc.info/docs/
      licence:
        - "GPL-3.0-or-later"
      identifier: biotools:multiqc
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'sample1', single_end:false ]
    - xml:
        type: file
        description: xml files from an Illumina sequencing run
        pattern: "*.xml"
        ontologies:
          - edam: http://edamontology.org/format_2332
    - interop_bin:
        type: file
        description: Illumina InterOp binary files
        pattern: "InterOp/*.bin"
        ontologies:
          - edam: http://edamontology.org/format_2333
    - extra_multiqc_files:
        type: file
        description: |
          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
        ontologies: []
    - multiqc_config:
        type: file
        description: Optional config yml for MultiQC
        pattern: "*.{yml,yaml}"
        ontologies:
          - edam: http://edamontology.org/format_3750
    - multiqc_logo:
        type: file
        description: Optional logo file for MultiQC
        pattern: "*.{png}"
        ontologies: []
    - replace_names:
        type: file
        description: |
          Optional two-column sample renaming file. First column a set of
          patterns, second column a set of corresponding replacements. Passed via
          MultiQC's `--replace-names` option.
        pattern: "*.{tsv}"
        ontologies:
          - edam: http://edamontology.org/format_3475
    - sample_names:
        type: file
        description: |
          Optional TSV file with headers, passed to the MultiQC --sample_names
          argument.
        pattern: "*.{tsv}"
        ontologies:
          - edam: http://edamontology.org/format_3475
output:
  report:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'sample1', single_end:false ]
      - "*.html":
          type: file
          description: MultiQC report file
          pattern: ".html"
          ontologies: []
  data:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'sample1', single_end:false ]
      - "*_data":
          type: directory
          description: MultiQC data dir
          pattern: "multiqc_data"
  plots:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'sample1', single_end:false ]
      - "*_plots":
          type: file
          description: Plots created by MultiQC
          pattern: "*_data"
          ontologies: []
  versions:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - multiqc:
          type: string
          description: The tool name
      - multiqc --version | sed "s/.* //g":
          type: eval
          description: The expression to obtain the version of the tool
  versions_interop:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - interop:
          type: string
          description: The tool name
      - python -c "import interop; print(interop.__version__)":
          type: eval
          description: The expression to obtain the version of the tool
  versions_multiqcsav:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - multiqcsav:
          type: string
          description: The name of the tool
      - python -c "import multiqc_sav; print(multiqc_sav.__version__)":
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@matthdsm"
  - "@delfiterradas"
maintainers:
  - "@matthdsm"