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Question: How to run R docker in WDL?
Entering edit mode

Hello community,

I am building a pipeline in WDL + Cromwell. I have a specific docker for each tasks, or example:

version 1.0 

import "../tasks/common.wdl"

task CallSV {
    input {
        IndexedBamFile bamFile
        Reference reference
        String outputPath    

    command <<< 
        delly call -o ~{outputPath}.bcf -g ~{reference.fasta} ~{bamFile.file}

    output {
        File dellyVcf = "~{outputPath}.bcf" 

    runtime {
        docker: ""


How do I go about building another task that runs a R script which requires a specific package (UpSetR) ?

Entering edit mode

It might make more sense to post this on StackExchange as it is a technical rather than a bioinformatics-related question.

ADD REPLYlink 10 months ago
Entering edit mode

Why not create a container with your script and its dependencies ?

ADD REPLYlink 10 months ago
Jean-Karim Heriche

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