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microbiomedata / mg_annotation

Metagenome Annotation Workflow
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update product mapping files #25

Closed aclum closed 6 months ago

aclum commented 7 months ago

We missed updating to the new product mapping tables when we updated to img annotation version 5.2. Update the workflow to use /global/cfs/cdirs/m3408/refdata/img/Product_Name_Mappings/20230814

This is what Marcel is now using.

cc @hubin-keio

aclum commented 6 months ago

@kaijli @Michal-Babins is there an update here? this needs to be updated before we start running workflows again.

ssarrafan commented 6 months ago

@hubin-keio brought this up at the sync today. @Michal-Babins @hubin-keio @aclum who should be part of this discussion?

aclum commented 6 months ago

Discussing the general issue of staying in sync with JGI is separate than fixing this specific issue. We can and should move forward with this fix so we can resume the workflows.

chienchi commented 6 months ago

The code in WDL use the latest symlink directory. So, I think we only need to update the refdata/img/Product_Name_Mappings/lastest symlink to point to 20230814, right? The workflow WDL itself doesn't need update and make new release.

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aclum commented 6 months ago

I think that is bad practice and part of the reason why we didn't catch that these hadn't been updated in the first place.

chienchi commented 6 months ago

I see. We should update the wdl and use the correct path and make a new release.

ssarrafan commented 6 months ago

I moved this to the next sprint. @aclum is this required for GSP?
FYI @chienchi @kaijli

aclum commented 6 months ago

yes b/c I'd like these fixed before we continue workflow processing.