Merge remote-tracking branch 'origin/update-existing-cohort-parser-wi…

…th-skip-flag' into update-existing-cohort-parser-with-skip-flag
populationgenomics · Nov 20, 2023 · 20af8c6 · 20af8c6
2 parents 2aec9dc + 9f0909c
commit 20af8c6
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/scripts/parse_existing_cohort.py b/scripts/parse_existing_cohort.py
@@ -223,7 +223,7 @@ def get_existing_external_sequence_ids(self, participant_map: dict[str, dict]):
     '--allow-missing-files',
     'allow_missing_files',
     is_flag=True,
-    help='Set this flag to parse manifests with missing data',
+    help='Set this flag to parse/ingest sequencing groups with missing reads',
 )
 @click.argument('manifests', nargs=-1)
 @run_as_sync

diff --git a/test/test_parse_existing_cohort.py b/test/test_parse_existing_cohort.py
@@ -238,7 +238,7 @@ async def test_existing_row(
 
     @run_as_sync
     async def test_get_read_filenames_no_reads_fail(self):
-        """Test when allow_missing_files is False and records with missing fastqs, ValueError is raised"""
+        """Test ValueError is raised when allow_missing_files is False and sequencing groups have no reads"""
 
         single_row = {Columns.MANIFEST_FLUID_X: ''}