Fail Avro extract and callset stats on bad filter name [VS-655] #8046
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there's already a task ValidateFilterSetName in GvsExtractCallset (see https://github.com/broadinstitute/gatk/blob/ah_var_store/scripts/variantstore/wdl/GvsExtractCallset.wdl#L117); perhaps these two tasks could be combined?
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## ah_var_store #8046 +/- ##
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Coverage ? 86.249%
Complexity ? 35205
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Files ? 2173
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Hits ? 142314
Misses ? 16362
Partials ? 6328 |
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| @@ -11,7 +11,16 @@ workflow GvsExtractAvroFilesForHail { | |||
| Int scatter_width = 10 | |||
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| call OutputPath { input: go = true } | |||
| call Utils.ValidateFilterSetName { | |||
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@rsasch gets the credit for suggesting this! 😄
| @@ -207,52 +207,11 @@ workflow GvsExtractCallset { | |||
| } | |||
| } | |||
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| task ValidateFilterSetName { | |||
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| echo "project_id = ~{query_project}" > ~/.bigqueryrc | ||
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| OUTPUT=$(bq --location=US --project_id=~{query_project} --format=csv query --use_legacy_sql=false ~{bq_labels} "SELECT filter_set_name as available_filter_set_names FROM \`~{data_project}.~{data_dataset}.filter_set_info\` GROUP BY filter_set_name") |
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Mind seeing if this works without the "--location=US" part and, if so, removing it? As is, it'll fail if we specify a dataset anywhere else. I'm 99.99% sure this call will function perfectly without that parameter.
FAILED runs with bad filter names:
Successful runs with good filter names: