removed ambiguous vdj tasks

airflow_var/var.json

@@ -36,7 +36,7 @@
   "woolf_server_hostname":"woolf.med.ic.ac.uk",
   "eliot_server_hostname":"eliot.med.ic.ac.uk",
   "igf_lims_server_hostname":"igf-lims.cc.ic.ac.uk",
-  "tenx_single_cell_immune_profiling_feature_types": {"gene_expression":"","vdj":"","vdj-t":"","vdj-b":"","antibody_capture":"","antigen_capture":"","crisper_guide_capture":""},
+  "tenx_single_cell_immune_profiling_feature_types": {"gene_expression":"","vdj-t":"","vdj-b":"","antibody_capture":"","antigen_capture":"","crisper_guide_capture":""},
   "scanpy_single_sample_template":"",
   "scanpy_notebook_image":"",
   "scirpy_single_sample_template":"",

dags/dag9_tenx_single_cell_immune_profiling.py

@@ -305,6 +305,7 @@ with dag:
   load_scanpy_report_for_sc_5p_to_db >> upload_scanpy_report_for_sc_5p_to_box
   run_scanpy_for_sc_5p >> upload_cellbrowser_for_sc_5p_to_ftp
   ## TASK
+  """
   run_scirpy_for_vdj = \
     PythonOperator(
       task_id='run_scirpy_for_vdj',
@@ -377,6 +378,7 @@ with dag:
   run_scirpy_for_vdj >> load_cellranger_vdj_matrics_to_db
   load_scirpy_report_for_vdj_to_db >> upload_scirpy_report_for_vdj_to_ftp
   load_scirpy_report_for_vdj_to_db >> upload_scirpy_report_for_vdj_to_box
+  """
   ## TASK
   run_scirpy_for_vdj_b = \
     PythonOperator(
@@ -1008,8 +1010,8 @@ with dag:
   upload_scanpy_report_for_sc_5p_to_ftp >> update_analysis_and_status
   upload_scanpy_report_for_sc_5p_to_box >> update_analysis_and_status
   upload_cellbrowser_for_sc_5p_to_ftp >> update_analysis_and_status
-  upload_scirpy_report_for_vdj_to_ftp >> update_analysis_and_status
-  upload_scirpy_report_for_vdj_to_box >> update_analysis_and_status
+  #upload_scirpy_report_for_vdj_to_ftp >> update_analysis_and_status            # no more ambiguous VDJ
+  #upload_scirpy_report_for_vdj_to_box >> update_analysis_and_status
   upload_scirpy_report_for_vdj_b_to_ftp >> update_analysis_and_status
   upload_scirpy_report_for_vdj_b_to_box >> update_analysis_and_status
   upload_scirpy_report_for_vdj_t_to_ftp >> update_analysis_and_status