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
      doi: ""
      licence: GPL-3

params:
  - parametrize:
      type: boolean
      description: If true, parametrize the notebook
  - implicit_params:
      type: boolean
      description: |
        If true (default), include the implicit params
          * `input_dir`, which points to the directory containing the files added via `input_files`,
          * `artifact_dir`, which points to the directory where the notebook should place output files, and
          * `cpus`, which contains the value of ${task.cpus}
  - meta_params:
      type: boolean
      description: |
        If true, include a parameter `meta` which contains the information specified
        via the `meta` input channel.

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}"
  - parameters:
      type: map
      description: |
        Groovy map with notebook parameters which will be passed to
        rmarkdown to generate parametrized reports.
  - input_files:
      type: path
      description: One or multiple files serving as input data for the notebook.
      pattern: "*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: HTML report generated from Rmarkdown
      pattern: "*.html"
  - session_info:
      type: file
      description: dump of R SessionInfo
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@grst"