Functionality: Adding sequencing-type as a parameter to allow ingestion of exome data #666
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…data comes along and sequencing groups can be ingested as exomes instead of defaulting to genome
vivbak
requested changes
Jan 28, 2024
scripts/parse_existing_cohort.py
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| @click.option( | ||
| '--sequencing-type', | ||
| type=click.Choice(['genome', 'exome']), | ||
| required=True, |
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Do we need to set required to be true? Esp since we have a default 'genome' described below
… default set to genome
…s set correctly in the ExistingCohortParser class when the --sequencing-type flag is set to 'genome' or 'exome'. The test checks both 'genome' and 'exome' options.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## dev #666 +/- ##
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+ Coverage 68.57% 68.67% +0.09%
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Files 131 131
Lines 10166 10198 +32
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+ Hits 6971 7003 +32
Misses 3195 3195 ☔ View full report in Codecov by Sentry. |
vivbak
approved these changes
Jan 28, 2024
test/test_parse_existing_cohort.py
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| @@ -280,3 +285,113 @@ async def test_get_read_filenames_no_reads_pass(self): | |||
| self.assertIn('No read files found for ', cm.output[0]) | |||
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| self.assertEqual(len(read_filenames), 0) | |||
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| @run_as_sync | |||
| async def test_exome_sequencing_type(self): | |||
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Maybe either rename or split into two so it's accurate to what we're testing
michael-harper
deleted the
add-exome-as-sequencing-type-to-be-ingested
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Adding sequencing-type as a parameter for future-proofing when exome data comes along and sequencing groups can be ingested as exomes instead of defaulting to genome.
At the moment, default_sequencing_type is set to genome, this fix would allow default_sequencing_type to be either exome or genome