Skip to content

fix for cellranger count path #184

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
avikdatta merged 1 commit into from
Mar 12, 2026
Merged

fix for cellranger count path #184

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 15 additions & 3 deletions igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -351,16 +351,28 @@ def run_cellranger_script(
def run_single_sample_scanpy(
sample_group: str,
cellranger_output_dir: str,
design_dict: dict) -> dict:
design_dict: dict,
count_dir: str = "count",
feature_bc_matrix_name: str = "sample_filtered_feature_bc_matrix.h5"
) -> dict:
try:
## set cellranger counts dir
cellranger_counts_dir = \
os.path.join(
cellranger_output_dir,
'outs',
'per_sample_outs',
sample_group,
'count')
sample_group)
if not os.path.exists(
os.path.join(
cellranger_counts_dir,
feature_bc_matrix_name
)
):
cellranger_counts_dir = os.path.join(
cellranger_counts_dir,
count_dir
)
## set scanpy dir
scanpy_output_dir = \
os.path.join(
Expand Down
Loading