Rework Hail script generation [VS-616] #8034
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mcovarr
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RoriCremer,
rsasch,
gbggrant and
koncheto-broad
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8034 +/- ##
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Coverage ? 43.628%
Complexity ? 21865
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Files ? 2173
Lines ? 165004
Branches ? 17792
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Hits ? 71988
Misses ? 87583
Partials ? 5433 |
rsasch
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gbggrant
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| import hail as hl | ||
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| unslashed_tmp_dir = tmp_dir if not tmp_dir.endswith('/') else tmp_dir[:-1] | ||
| hl.init(tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_general') |
RoriCremer
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| vqsr_tranche_data=args('vqsr_tranche_data'), | ||
| reference_genome=rg38, | ||
| final_path=vds_output_path, | ||
| tmp_dir=f'{unslashed_tmp_dir}/hail_tmp_import_gvs' |
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this is where we will put:
intermediate_resume_point=x
and also do we want to add:
partitions_per_sample=0.4,
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Github actions tests reported job failures from actions build 3146642435
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Github actions tests reported job failures from actions build 3153749161
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This was referenced Mar 17, 2023
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Splits the original script GVS to Hail import script into two smaller scripts. The first script creates the "MVP" Hail VariantDataset (VDS), the second script implements all further AC/AN/AF and VAT input processing. No Avro file literals are embedded in either script so both scripts are much smaller than the previous single script they replace.
Successful Quickstart run here: https://app.terra.bio/#workspaces/gvs-dev/mlc%20GVS%20Quickstart%20v3/job_history/2e4f192f-1042-4ee5-b1e3-3c00c97e620b
VDS generated from this script: gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/2e4f192f-1042-4ee5-b1e3-3c00c97e620b/GvsExtractAvroFilesForHail/4124ba9e-4220-47f4-af46-8a8f1ba9ca66/call-OutputPath/2022-09-23-74fb33b4/gvs_export.vds
Tieout VCF generated from this VDS: gs://fc-a1621719-20ea-471d-a0ef-a41383dc76bd/submissions/2e4f192f-1042-4ee5-b1e3-3c00c97e620b/GvsExtractAvroFilesForHail/4124ba9e-4220-47f4-af46-8a8f1ba9ca66/call-OutputPath/2022-09-23-74fb33b4/tieout.vcf