nf-core-modules/modules/nf-core/rmarkdownnotebook/meta.yml at f96c67d6fd87fd8dbfe104dfc5a95a5115fec4b7 · mahesh-panchal/nf-core-modules · GitHub

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name: rmarkdownnotebook
description: Render an rmarkdown notebook. Supports parametrization.
keywords:
  - R
  - notebook
  - reports
tools:
  - rmarkdown:
      description: Dynamic Documents for R
      homepage: https://rmarkdown.rstudio.com/
      documentation: https://rmarkdown.rstudio.com/lesson-1.html
      tool_dev_url: https://github.com/rstudio/rmarkdown
      licence:
        - "GPL-3"
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - notebook:
        type: file
        description: Rmarkdown file
        pattern: "*.{Rmd}"
        ontologies:
          - edam: http://edamontology.org/format_4000
  - parameters:
      type: map
      description: |
        Groovy map with notebook parameters which will be passed to
        rmarkdown to generate parametrized reports.
  - input_files:
      type: file
      description: One or multiple files serving as input data for the notebook.
      pattern: "*"
      ontologies: []
output:
  report:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.html":
          type: file
          description: HTML report generated from Rmarkdown
          pattern: "*.html"
          ontologies: []
  parameterised_notebook:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.parameterised.Rmd":
          type: file
          description: Parameterised Rmarkdown file
          pattern: "*.parameterised.Rmd"
          ontologies:
            - edam: http://edamontology.org/format_4000
  artifacts:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - artifacts/*:
          type: file
          description: Artifacts generated by the notebook
          pattern: "artifacts/*"
          ontologies: []
  session_info:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - session_info.log:
          type: file
          description: dump of R SessionInfo
          pattern: "*.log"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750
authors:
  - "@grst"
maintainers:
  - "@grst"