Entering edit mode
5.7 years ago
c.clarido
▴
110
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: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
}
}
How do I go about building another task that runs a R script which requires a specific package (UpSetR) ?
It might make more sense to post this on StackExchange as it is a technical rather than a bioinformatics-related question.
Why not create a container with your script and its dependencies ?