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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Bug: Can't detect 'path' not set for a resource or program #50

Closed biocyberman closed 9 years ago

biocyberman commented 9 years ago

I took me a while to pinpoint the issue.

Currently path is not set for snpEffReference resource in uppmax_global_config.xml. This causes a vague java.lang.NullPointerException. After debugging, I found that method transformToNamePathMap could not map snpEffReference resource correctly, and the exception in getVersionFromKey is never thrown. Probably exceptions have to be catched in the trait NameVersionAndPath, but I have no ideas how to do that yet. One quick fix is to make sure that path to snpEffReference resource is set in uppmax_global_config.xml

johandahlberg commented 9 years ago

This is fixed in the devel branch already. Will merge that as soon as I get confirmation from @parlundin on some other things.

biocyberman commented 9 years ago

Thank you @johandahlberg. I only pulled and checked on the master branch so I did not know the bug has been fixed. I will close this then.