Question: How to run R docker in WDL?
gravatar for c.clarido
16 months ago by
Netherlands/Rotterdam/Leiden University (Applied Science)
c.clarido60 wrote:

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) ?

gatk docker cromwell R wdl • 570 views
ADD COMMENTlink written 16 months ago by c.clarido60

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

ADD REPLYlink written 16 months ago by ATpoint36k

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

ADD REPLYlink written 16 months ago by Jean-Karim Heriche23k
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