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Vs 629 failure to retrieve job information during ingest #8047
Vs 629 failure to retrieve job information during ingest #8047
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…ll remove after testing)
…ll remove after testing)
…test the python changes
…r GvsCreateFilterSet
…that is not available in all locations
…nch (and thus the python scripts in which I fixed location issues on this branch)
…mation-during-ingest Manually chose my newer docker image over the others. Note: will need to produce a slim (or alpine) version of my docker images, as I expect more merge conflicts with the PR for VS-648
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8047 +/- ##
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Coverage ? 16.953%
Complexity ? 4702
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Files ? 1375
Lines ? 82247
Branches ? 13121
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Hits ? 13943
Misses ? 66245
Partials ? 2059 |
This PR contains several distinct modifications necessary to protect our pipeline against errors when a location is specified on a BQ dataset
Only partially related, this PR also contains the creation of the script/variantstore/utils directory to hold useful scripts, and the useful pushGATKtoGCS script for pushing jars to an easily-referenced location for WDLs (h/t to Miguel) The entire tragic history of successes and failures can be seen in the job history of the workspace https://app.terra.bio/#workspaces/gvs-dev/GVS%20Tiny%20Quickstart%20hatcher/job_history Every stage of the quickstart can be verified within to--eventually and only after the gods deemed my suffering sufficient--have passed. |
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Looks great! Only a couple of very minor nits
src/main/java/org/broadinstitute/hellbender/tools/gvs/filtering/ExtractFeaturesBQ.java
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…as recently updated to
… not newest GATK image)
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one minor update requested
hardening standard quickstart pipeline against errors when a location is specified