fix for cellranger output path

imperial-genomics-facility · Nov 24, 2023 · c535449 · c535449
1 parent c122c46
commit c535449
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Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py b/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py
@@ -159,7 +159,7 @@ def prepare_cellranger_script(sample_group: str, design_dict: dict) -> dict:
       prepare_cellranger_run_dir_and_script_file(
         sample_group=str(sample_group),
         work_dir=work_dir,
-        output_dir=os.path.join(work_dir, str(sample_group))
+        output_dir=os.path.join(work_dir, str(sample_group)),
         design_file=design_file,
         db_config_file=DATABASE_CONFIG_FILE,
         run_script_template=CELLRANGER_MULTI_SCRIPT_TEMPLATE)

diff --git a/test/igf_airflow/test_dag34_cellranger_multi_scRNA_utils.py b/test/igf_airflow/test_dag34_cellranger_multi_scRNA_utils.py
@@ -264,6 +264,7 @@ def test_prepare_cellranger_run_dir_and_script_file(self):
       prepare_cellranger_run_dir_and_script_file(
         sample_group="grp1",
         work_dir=temp_dir,
+        output_dir=os.path.join(temp_dir, "grp1"),
         design_file=self.yaml_file,
         db_config_file=self.dbconfig,
         run_script_template='template/cellranger_template/cellranger_multi_run_script_v1.sh')