Added workaround to Nextflow baseDir bug on kubernetes #167
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bentsherman
requested review from
JohnHadish and
spficklin
and removed request for
JohnHadish
|
Since this PR only affects the k8s profile and we need these changes to run GEMmaker more easily on kubernetes, I will go ahead and merge. |
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The trimmomatic clip_path parameter uses
${baseDir}which does not work on kubernetes, refer to the issue I created with Nextflow a while back: nextflow-io/nextflow#1050This PR adds a little workaround that avoids using
${baseDir}when using kubernetes. It's contained in thek8sprofile so it won't affect other environments. I also fixed a couple of weird things I saw with some of the comments but let me know if that was in error and I'll revert them.Also I've tested this fix on the PRP and it works. :)