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@@ -307,81 +307,6 @@ with dag:
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load_scanpy_report_for_sc_5p_to_db >> upload_scanpy_report_for_sc_5p_to_box
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run_scanpy_for_sc_5p >> upload_cellbrowser_for_sc_5p_to_ftp
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## TASK
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- """
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- run_scirpy_for_vdj = \
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- PythonOperator(
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- task_id='run_scirpy_for_vdj',
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- dag=dag,
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- queue='hpc_4G',
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- python_callable=run_singlecell_notebook_wrapper_func,
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- params={'cellranger_xcom_key':'cellranger_output',
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- 'cellranger_xcom_pull_task':'run_cellranger',
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- 'scanpy_timeout':1200,
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- 'allow_errors':False,
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- 'kernel_name':'python3',
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- 'analysis_name':'scirpy',
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- 'vdj_dir':'vdj',
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- 'count_dir':'count',
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- 'output_notebook_key':'scirpy_notebook',
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- 'analysis_description_xcom_pull_task':'fetch_analysis_info',
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- 'analysis_description_xcom_key':'analysis_description'})
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- load_cellranger_vdj_matrics_to_db = \
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- PythonOperator(
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- task_id='load_cellranger_vdj_matrics_to_db',
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- dag=dag,
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- queue='hpc_4G',
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- python_callable=load_cellranger_metrices_to_collection,
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- params={'cellranger_xcom_key':'cellranger_output',
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- 'cellranger_xcom_pull_task':'run_cellranger',
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- 'collection_type':'CELLRANGER_MULTI',
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- 'collection_name_task':'load_cellranger_result_to_db',
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- 'collection_name_key':'sample_igf_id',
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- 'metrics_summary_file':'vdj/metrics_summary.csv',
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- 'attribute_prefix':'CELLRANGER_VDJ'})
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- load_scirpy_report_for_vdj_to_db = \
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- PythonOperator(
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- task_id='load_scirpy_report_for_vdj_to_db',
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- dag=dag,
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- queue='hpc_4G',
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- python_callable=load_analysis_files_func,
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- params={'collection_name_task':'load_cellranger_result_to_db',
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- 'collection_name_key':'sample_igf_id',
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- 'file_name_task':'run_scirpy_for_vdj',
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- 'file_name_key':'scirpy_notebook',
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- 'analysis_name':'scirpy_vdj',
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- 'collection_type':'SCIRPY_VDJ_HTML',
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- 'collection_table':'sample',
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- 'output_files_key':'output_db_files'})
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- upload_scirpy_report_for_vdj_to_ftp = \
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- PythonOperator(
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- task_id='upload_scirpy_report_for_vdj_to_ftp',
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- dag=dag,
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- queue='hpc_4G',
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- python_callable=ftp_files_upload_for_analysis,
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- params={'xcom_pull_task':'load_scirpy_report_for_vdj_to_db',
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- 'xcom_pull_files_key':'output_db_files',
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- 'collection_name_task':'load_cellranger_result_to_db',
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- 'collection_name_key':'sample_igf_id',
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- 'collection_type':'FTP_SCIRPY_VDJ_HTML',
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- 'collection_table':'sample',
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- 'collect_remote_file':True})
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- upload_scirpy_report_for_vdj_to_box = \
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- PythonOperator(
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- task_id='upload_scirpy_report_for_vdj_to_box',
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- dag=dag,
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- queue='hpc_4G',
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- python_callable=upload_analysis_file_to_box,
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- params={'xcom_pull_task':'load_scirpy_report_for_vdj_to_db',
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- 'xcom_pull_files_key':'output_db_files',
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- 'analysis_tag':'scirpy_vdj_single_sample_report'})
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- ## PIPELINE
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- decide_analysis_branch >> run_scirpy_for_vdj
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- run_scirpy_for_vdj >> load_scirpy_report_for_vdj_to_db
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- run_scirpy_for_vdj >> load_cellranger_vdj_matrics_to_db
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- load_scirpy_report_for_vdj_to_db >> upload_scirpy_report_for_vdj_to_ftp
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- load_scirpy_report_for_vdj_to_db >> upload_scirpy_report_for_vdj_to_box
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- """
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- ## TASK
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run_scirpy_for_vdj_b = \
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PythonOperator(
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task_id='run_scirpy_for_vdj_b',
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