This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
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