The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Recommended way of shipping custom scripts with WDL pipelines?
Is there a recommended way to ship a custom script with a WDL pipeline?
I'm writing a WDL workflow executing a step running R code using
Rscript. The CWL version of this pipeline was doing something like this:
baseCommand: Rscript requirements: - class: InitialWorkDirRequirement listing: - $(inputs.script) inputs: script: type: File inputBinding: position: 1 default: class: File location: MyScript.R
This allows me to ship my R code right next to my
.cwl file. Is there something similar with WDL? I would like to avoid hard-coding paths or assuming the script is in the user