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RMarkdown Docker step

Work in progress

Parameters

Parameter	Required	Description
rmd	yes	The filename of your RMarkdown script (*.Rmd)
params	no	Input parameters that can be used inside the RMarkdown script (e.g. input files)
output	yes	The name and location of the rendered HTML page.
image	no	Custom Docker image.

Examples

Example 1

id: rmarkdown-example
name: RMarkdown Example
version: 1.0
workflow:
  steps:
    - name: Running report script
      type: rmd_docker
      rmd: report.Rmd
      params: $dataset
      output: ${report}.html
  inputs:
    - id: dataset
      description: Dataset
      type: hdfs_file
  outputs:
    - id: report
      description: Report
      type: local_file

Example 2

Run a report script only when Docker is installed:

id: rmarkdown-example
name: RMarkdown Example
version: 1.0
workflow:
  steps:
#if (${docker_installed} == "true")
    - name: Running RMD in Docker Container
      type: rmd_docker
      rmd: report.Rmd
      output: ${report}.html
#end

  outputs:
    - id: report
      description: Report
      type: local_file