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

name: r markdown 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:

name: rmd-docker
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