Vs 299 spike speed up integration tests #8706
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* VS-815: Add Support for YNG to VQSR Lite * Up the memory of a task in JointVcfFiltering.wdl. * Use 'HDD' rather than 'LOCAL' in JointVcfFiltering.wdl
* Update GvsCalculatePrecisionAndSensitivity.wdl to allow for different scale of calibration_sensitivity vs. lod score. Also retrieving score from JointVcfFiltering and storing that in BQ and in the VCF.
* deleted VDS * only one left
…tion of Delta (#8205) * Lees name * add vds validation script written by Tim * fix rd tim typo * make sure temp dir is set and not default for validate() * swap to consistent kebab case Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com> * clean up validation * put init in the right place * add proper example to notes * update code formatting --------- Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
* Lees name * add vds validation script written by Tim * fix rd tim typo * make sure temp dir is set and not default for validate() * swap to consistent kebab case Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com> * clean up validation * put init in the right place * add proper example to notes * update code formatting * update review --------- Co-authored-by: Miguel Covarrubias <mcovarr@users.noreply.github.com>
* Don't run gatk tests when the only changes in a commit are in the scripts/variantstore directory.
* laying framework for FOFN bulk import code * adding in terra notebook utils code * updating wdl * updating environment variables to make this work better * quotey McBetterQuotes * extra environment variables * normalizing variable name with other wdls that require it * gotta explicitly set WORKSPACE_NAMESPACE to the google project as well. Apparently. * typoooooooooooooooooo * Didn't pipe the output files the entire way up * whoopsie * typo * two updates after testing: 1. We do NOT want to assume that the sample ids we want are in the name field. Pass that through as a parameter. 2. We want to explicitly pause every 500 samples, as that's our page size. It slows our requests down enough to not spam the backend server and hit 503 errors, although it does slow down the rate at which we can write the files if the dataset is too big. Which shouldn't be a concern, because as long as it doesn't cause errors it is still a hands off process. 3. We want to account to heterogenous data. In AoU Delta, for instance, the control samples keep their vcf and vcf_index data in a different field. This would cause the whole thing to fail if we weren't accounting for that explicitly, and now we generate an errors.txt file that will hold the row that we couldn't find the correct columns for so they can be examined later * silly mistake copying the functioning code over from the workbook * making script more robust against specifying imaginary columns in the data table and being slightly more informative in the output of the python script * increasing the size of the disk this is running on for the sake of efficiency (and handling larger callsets) * Passing errors up * update params * short term testing (rate lim) * make it only 25 shards! * add workspace id scraping * add workspace id scraping fixup * this is not functioning--need to curl in the wdl * clean up vcfs so we dont run out of space * add duplicates test to the shard loading * clean up namespace prep --------- Co-authored-by: Aaron Hatcher <hatcher@broadinstitute.org>
* Use the annotation 'AS_MQ' for indels.
… table (#8278) * Remove the unneeded SCORE field from the filter_set_info_vqsr table * Updated the docker images.
* add queries for testing mismatched sites and variants across possible duplicates * still need to wire these through * plumb thru dup validation * dockstore for testing * update docker * add xtrace * better bool logic * clean up bash * okay lets try ripping shit out to get this to work * okay lets put a few lines back * ok that worked, lets swap for better errors * short term remove clinvar * review changes * update docker * explain removal of clinvar test
* Adding tests for ExtractCohortLite.
* Simple fix to have the header of the VAT tsv to use tab characters.
* Updated to latest version of VQSR Lite (from Master) * Ported tests and files for VQSR Lite over * Refactored VQSR Classic code into its own WDL
* add a brief quota request template doc * link quota request template * add header stream info * becs suggestions * discuss load_data_batch * header info * becs formatting improvements * add aarons calculations notes
* Add task to deduplicate the VAT table.
…emory or disk on certain task. (#8704)
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This was for a spike, so this draft PR is never going to be actually merged. But having it in this format will be helpful for whoever picks the work up next!