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EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure
Apache License 2.0
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Harmonisation pipeline did not use the right unmapped data to generate harmonisation log file #1316

Closed jiyue1214 closed 3 days ago

jiyue1214 commented 1 month ago

Yue followed Karatug's script to run the harmonisation pipeline on LSF and Slurm. She found the LSF pipeline used GCST90293086's unmapped file to generate GCST90293085's harmonisation log file. All other files are correct. Need to figure out the reason causing it.

jiyue1214 commented 1 month ago

Where the script and intermediates files are: /nfs/production/keane/amp/AMP_harmonization/harmonization/test/Karatug_LSF_Slurm/LSF

jiyue1214 commented 2 weeks ago

Generating harmonisation log is the last step of the whole pipeline, which inputs are two channel, harmonisation channel, and unmapped channel. harmonisation channel has id GCST, while unmapped channel perviously only contains path of unmapped file. I have improved the unmapped channel that to make sure it also checks the GCST_id while generating the log file.

This ticket can be moved to review channel and then close when Karatug finish testing the new release.

jiyue1214 commented 1 week ago

Can be closed