Return non-zero exit code when annotation pipeline fails

genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API

MIT License

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Return non-zero exit code when annotation pipeline fails #270

Closed jamesqo closed 8 months ago

jamesqo commented 8 months ago

This PR adds a reliable way of checking whether or not the Genome Nexus pipeline failed from the command line. It is needed for the NCI work because we want to distinguish the cases where it is an annotation issue (eg. missing variants) or with the GN code itself.

/cc @averyniceday @leexgh @inodb