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V4 variants data pipeline: add task for CAIDs annotation #1429

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merged 3 commits into from
Mar 1, 2024

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nadeaujoshua
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This PR is a continuation of the work started in #1419. It adds a task to the V4 variants pipeline to add ClinGen Canonical Allele IDs (CAIDs) to the variants dataset. It uses the output CAIDs Hail table from #1419 to do so.

Originally, the pipeline was written to do this work in step 2 of the pipeline, but the adding of CAIDs was bypassed during the V4 release because the CAIDs Hail table was not yet created.

Now that the table is ready to use for annotating the variants dataset, it would be easier to do by adding a new step (4) to the end of the pipeline to simply use the output of step 3 (current state of the variants dataset). Alternatively, re-running the pipeline as originally written (add CAIDs in step 2) would require running more steps and overwriting the existing outputs, specifically steps 2 and 3.

@nadeaujoshua nadeaujoshua marked this pull request as ready for review March 1, 2024 19:06
@nadeaujoshua nadeaujoshua requested review from a team, sjahl, mattsolo1, rileyhgrant and phildarnowsky-broad and removed request for a team and sjahl March 1, 2024 19:08
@nadeaujoshua nadeaujoshua merged commit 64e4492 into main Mar 1, 2024
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@nadeaujoshua nadeaujoshua deleted the jn/variants-pipeline-add-caids branch March 1, 2024 20:39
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