From 81644b06fb2256fd0b6ffa4e297fcad5a73c3c55 Mon Sep 17 00:00:00 2001
From: Vivian Bakiris <79084890+vivbak@users.noreply.github.com>
Date: Tue, 13 Feb 2024 09:35:02 +1100
Subject: [PATCH] Fix Existing Cohort Parser Sequencing Type Param (#679)

* Fix click overwriting param to None when not specified

* Fix whitespace after : for the linter
---
 scripts/parse_existing_cohort.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/parse_existing_cohort.py b/scripts/parse_existing_cohort.py
index 2603a8d60..1df35063c 100644
--- a/scripts/parse_existing_cohort.py
+++ b/scripts/parse_existing_cohort.py
@@ -216,6 +216,7 @@ def get_existing_external_sequence_ids(self, participant_map: dict[str, dict]):
     '--sequencing-type',
     type=click.Choice(['genome', 'exome']),
     help='Sequencing type: genome or exome',
+    default='genome',
 )
 @click.option('--search-location', 'search_locations', multiple=True)
 @click.option(
@@ -239,11 +240,11 @@ async def main(
     project: str,
     search_locations: List[str],
     batch_number: Optional[str],
+    sequencing_type: str,
     confirm=True,
     dry_run=False,
     include_participant_column=False,
     allow_missing_files=False,
-    sequencing_type: str = 'genome',
 ):
     """Run script from CLI arguments"""