Rmarkdown#

Add to module run order:
#BioModule biolockj.module.diy.Rmarkdown

Description#

Render a custom R markdown.

Properties#

Properties are the name=value pairs in the configuration file.

Rmarkdown properties:#

Property	Description
rmarkdown.resources	list of file paths path to one or more files to be copied to the module resource folder. default: null
rmarkdown.rmarkdown	file path path to an R markdown file (.Rmd) to be rendered. default: null

General properties applicable to this module:#

Property	Description
cluster.batchCommand	string Terminal command used to submit jobs on the cluster default: null
cluster.jobHeader	string Header written at top of worker scripts default: null
cluster.modules	list List of cluster modules to load at start of worker scripts default: null
cluster.prologue	string To run at the start of every script after loading cluster modules (if any) default: null
cluster.statusCommand	string Terminal command used to check the status of jobs on the cluster default: null
docker.saveContainerOnExit	boolean If Y, docker run command will NOT include the --rm flag default: null
docker.verifyImage	boolean In check dependencies, run a test to verify the docker image. default: null
exe.Rscript	executable Path for the "Rscript" executable; if not supplied, any script that needs the Rscript command will assume it is on the PATH. default: null
script.defaultHeader	string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash
script.numThreads	integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8
script.numWorkers	integer Set number of samples to process per script (if parallel processing) default: 1
script.permissions	string Used as chmod permission parameter (ex: 774) default: 770
script.timeout	integer Sets # of minutes before worker scripts times out. default: null

Details#

version: 0.0.0 none

Adds modules#

pre-requisite modules
none found
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

rocker/r-rmd:latest

This can be modified using the following properties:
Rmarkdown.imageOwner
Rmarkdown.imageName
Rmarkdown.imageTag

Citation#

Module created by Ivory Blakley
BioLockJ v1.4.2