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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Running into error while running wdl workflow for infercnv on terra #539

Open smk5g5 opened 1 year ago

smk5g5 commented 1 year ago

Hi,

I copied the workflow from the terra workspace link provided. And everytime I run the workflow I keep getting 1inferCNV.R : command not found` error. I am not sure why is this the case. Is there a specific docker image I need to provide to it to make it work?

Thank you!

/cromwell_root/script: line 30: inferCNV.R: command not found

GeorgescuC commented 1 year ago

Hi @smk5g5 ,

This was an issue on my end when building the new Docker image, for some reason the line that added the CLI script to the path got interpreted as a comment so the script could not be found. You should now be able to get the workflow running by simply changing the docker_tag optional argument to "1.16.0-multiarch". At the moment the 1.16.0 and latest tags don't use the needed architecture to run on Terra so avoid those, but I'm trying to find the best solution for those tags.

Regards, Christophe.

GeorgescuC commented 1 year ago

The 1.16.0 and latest docker tags now work on Terra, and the CLI has been updated to support all arguments for run().