jbang exceptions while running on cloud about nf-gwas HOT 4 CLOSED

Hi Abhinav,
Great to see you're trying to run this on Azure. Thanks for the detailed error description and suggested solutions. Bundling the JARs into the docker container makes sense to us, feel free to move on with this. Let us know if there is input required from our side.

Collaboration sounds great, we would love to improve the pipeline that it runs smoothly on Azure.

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Thx for the detailed explanation. Right, conda is currently not supported, so approach sounds good to me. Really appreciate your work.

from nf-gwas.

Thanks @seppinho

Yes, I'd appreciate some thoughts on the overall manner we get this done.

As you might have noticed in the PR #46

1. I had to tweak the location of the JAR file within the container /opt/RegenieValidateInput.jar, so that it's available in a centralized location. When Nextflow mounts the task directory volume, this location can be accessed within the container.

2. I also tweaked the inputs of validate_phenotypes.nf as it would no longer rely upon the JAR being staged via channel.

3. Disabled the CACHE_JBANG_SCRIPTS process as its not serving the purpose in cloud context.

However, these changes mean that any non-containerized (in this case docker) workload would not find the expected JARs there. As the pipeline isn't officially supporting conda based setup then I'm guessing the above changes would be okay?

P.S. I have also explored the approach of staging the lib folder across the pipeline here (on internal PR of my fork) but ran across some issues there.

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Thanks! #46 has now been merged.

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