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RMarkdown step

To give the user feedback on the results of an executed workflow, it is important to summarize them in user-friendly reports containing plots, tables and other visualizations. Cloudgene supports the integration of R scripts that can be formatted using RMarkdown in order to render HTML sites.

Parameters

Parameter	Required	Description
rmd2	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.
include	yes	Use renderer HTML page as step's output (default: false).

Examples

Reports

Create html report:

id: rmarkdown-example
name: RMarkdown Example
version: 1.0
workflow:
  steps:
    - name: Running report script
      rmd2: report.Rmd
      params: $dataset
      output: ${report}.html
  inputs:
    - id: dataset
      description: Dataset
      type: hdfs_file
  outputs:
    - id: report
      description: Report
      type: local_file

HTML-Widgets

Use RMarkdown to generate html-widget and use it as step's output:

id: rmarkdown-example
name: RMarkdown Example
version: 1.0
workflow:
  steps:
    - name: Running report script
      rmd2: leaflet.Rmd
      params: $dataset
      output: ${report}.html
      include: true
  outputs:
    - id: report
      description: Report
      type: local_file

leaflet:

---
output:
  html_document:
    theme: null
    self_contained: true
---
```{r leaflet, echo=FALSE}
library(leaflet)
m <- leaflet() %>%
  addTiles() %>%  # Add default OpenStreetMap map tiles
  addMarkers(lng=174.768, lat=-36.852, popup="The birthplace of R")
m  # Print the map
 ```