change for bam to cram conv

dags/dag9_tenx_single_cell_immune_profiling.py

@@ -522,16 +522,18 @@ with dag:
       dag=dag,
       queue='hpc_4G4t',
       python_callable=convert_bam_to_cram_func,
-      params={'xcom_pull_files_key':'cellranger_output',
-              'xcom_pull_task':'run_cellranger',
-              'analysis_description_xcom_pull_task':'fetch_analysis_info',
-              'analysis_description_xcom_key':'analysis_description',
-              'use_ephemeral_space':True,
-              'threads':4,
-              'analysis_name':'cellranger',
-              'collection_type':'ANALYSIS_CRAM',
-              'collection_table':'sample',
-              'cram_files_xcom_key':'cram_files'})
+      params={
+        'xcom_pull_files_key': 'cellranger_output',
+        'xcom_pull_task': 'run_cellranger',
+        'analysis_description_xcom_pull_task': 'fetch_analysis_info',
+        'analysis_description_xcom_key': 'analysis_description',
+        'use_ephemeral_space': True,
+        'threads': 4,
+        'cellranger_bam_path': 'count/sample_alignments.bam',
+        'analysis_name': 'cellranger',
+        'collection_type': 'ANALYSIS_CRAM',
+        'collection_table': 'sample',
+        'cram_files_xcom_key': 'cram_files'})
   ## PIPELINE
   decide_analysis_branch >> convert_cellranger_bam_to_cram
   ## TASK