add sample qc task and filter_flags #1034
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bpblanken
reviewed
Feb 6, 2025
bpblanken
reviewed
Feb 6, 2025
jklugherz
changed the title
bpblanken
reviewed
Feb 13, 2025
jklugherz
commented
Feb 14, 2025
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| class WriteSampleQCJsonTaskTest(MockedDatarootTestCase): | ||
| @patch('v03_pipeline.lib.tasks.write_sample_qc_json.WriteTDRMetricsFilesTask') |
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I was not able to figure out the bigquery function mock contamination that was happening when this test was run with WriteSexCheckTableTaskTest, so I just mocked the entire WriteTDRMetricsFilesTask 🤷
bpblanken
reviewed
Feb 19, 2025
| sample_qc_dict = defaultdict(dict) | ||
| for row in ht.flatten().collect(): | ||
| r = dict(row) | ||
| sample_id = r.pop('s') |
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might be cleaner as
for field, value in r.items():
sample_qc_dict[r.pop('s')][field] = value
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idt this is possible RuntimeError: dictionary changed size during iteration
jklugherz
commented
Feb 19, 2025
bpblanken
reviewed
Feb 25, 2025
v03_pipeline/lib/misc/io.py
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| @@ -244,6 +244,17 @@ def import_imputed_sex(imputed_sex_path: str) -> hl.Table: | |||
| return ht.key_by(ht.s) | |||
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| def import_tdr_qc_metrics(file_path: str) -> hl.Table: | |||
| ht = hl.import_table(file_path) | |||
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I think there’s a way to define the types for non-strings at import time, we should try that!
v03_pipeline/lib/paths.py
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| dataset_type, | ||
| ), | ||
| 'sample_qc', | ||
| f'{hashlib.sha256(callset_path.encode("utf8")).hexdigest()}.json', |
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There’s the new “callset_path_hash” function that snuck in after this was started. We can use it here!
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adds sample_qc luigi task with a single metric - filter_flags - that outputs a json file, makes it a dependency of the write callset task, and adds the sample qc json to the metadata json.