VS-567. Removing usage of ServiceAccount from CreateVat related WDLs #7974
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Fix WDL error
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7974 +/- ##
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Coverage ? 79.218%
Complexity ? 33309
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Files ? 2173
Lines ? 165016
Branches ? 17793
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Hits ? 130723
Misses ? 28119
Partials ? 6174 |
| # { | ||
| # localization_optional: true | ||
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| # } |
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any reason not to just fully rip this out?
| gsutil cp ~{inputFileofFileNames} ~{updated_input_files} | ||
| fi | ||
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| # nothing to do - it is just reading the lines from the input - TODO - is there a better way to do this? |
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This was definitely written for the singular use case that is AoU annotation files are in GCP and I want to run them through the python script to transform them into the VAT schema
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I dont see any reason to have this task at all --and I dont think you need to worry about testing this WDL (maybe we even want to retire it?) since it will be used so rarely and if it is used again it will be in another emergency state that will probably require similar customization
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Okay, I've removed this file (as Bec mentioned, it's still in the github history).
…oveSAFromGvsCreateVAT
Bake the schema json into the docker file.
| cp ~{vat_schema_json_filepath} ~{vat_schema_json_filename} | ||
| cp ~{variant_transcript_schema_json_filepath} ~{variant_transcript_schema_json_filename} | ||
| cp ~{genes_schema_json_filepath} ~{genes_schema_json_filename} |
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Is this just cping all these to .? Could all of this be simplified to something like
ln /data/variant_annotation_table/schema/* .There was a problem hiding this comment.
Had to go back to using a cp - even ln -s wouldn't work (cromwell couldn't resolve/delocalize the outputs)
| String schema_filepath = "/data/variant_annotation_table/schema/" | ||
| String vat_schema_json_filename = "vat_schema.json" | ||
| String variant_transcript_schema_json_filename = "vt_schema.json" | ||
| String genes_schema_json_filename = "genes_schema.json" |
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this is awesome--thank you!
Removing usage of ServiceAccount from CreateVat related WDLs.