From decb679cf3cddec27fad5d3aa242d7e1fdf6ce3f Mon Sep 17 00:00:00 2001 From: Avik Datta Date: Sun, 18 Jan 2026 23:01:55 +0000 Subject: [PATCH 1/2] fixed scanpy notebook generation for dag34 --- igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py b/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py index f81b3c2e..a5b5d0cf 100644 --- a/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py +++ b/igf_airflow/utils/dag34_cellranger_multi_scRNA_utils.py @@ -457,6 +457,7 @@ def prepare_and_run_scanpy_notebook( scanpy_config: dict, timeout: int = 1200, kernel_name: str = 'python', + large_data: bool = False, allow_errors: bool = False) -> Tuple[str, str]: try: scanpy_h5ad = \ @@ -483,7 +484,8 @@ def prepare_and_run_scanpy_notebook( 'MITO_PREFIX': scanpy_config.get('MITO_PREFIX') or 'MT-', 'RUN_CELLCYCLE_SCORE': scanpy_config.get('RUN_CELLCYCLE_SCORE') or False, 'S_GENES':s_genes, - 'G2M_GENES': g2m_genes + 'G2M_GENES': g2m_genes, + 'LARGE_DATA': large_data } ## update input params and check paths singularity_image = \ @@ -740,7 +742,8 @@ def merged_scanpy_report( analysis_name=analysis_name, cellranger_group_id=str(sample_group), cellranger_counts_dir=cellranger_aggr_counts_dir, - scanpy_config=scanpy_config) + scanpy_config=scanpy_config, + large_data=True) target_notebook = \ os.path.join( scanpy_dir, From 8a62bc5a67bc508f96afb8dd0c335d64335a9eeb Mon Sep 17 00:00:00 2001 From: Avik Datta Date: Sun, 18 Jan 2026 23:06:41 +0000 Subject: [PATCH 2/2] updated dag36 --- igf_airflow/utils/dag36_cellranger_arc_scRNA_multiome_utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/igf_airflow/utils/dag36_cellranger_arc_scRNA_multiome_utils.py b/igf_airflow/utils/dag36_cellranger_arc_scRNA_multiome_utils.py index ab10daed..c36afd1f 100644 --- a/igf_airflow/utils/dag36_cellranger_arc_scRNA_multiome_utils.py +++ b/igf_airflow/utils/dag36_cellranger_arc_scRNA_multiome_utils.py @@ -589,7 +589,8 @@ def merged_scanpy_report_for_arc( analysis_name=analysis_name, cellranger_group_id=str(sample_group), cellranger_counts_dir=cellranger_aggr_counts_dir, - scanpy_config=scanpy_config) + scanpy_config=scanpy_config, + large_data=True) target_notebook = \ os.path.join( scanpy_dir,