added picard tasks

dags/dag9_tenx_single_cell_immune_profiling.py

@@ -19,6 +19,7 @@ from igf_airflow.utils.dag9_tenx_single_cell_immune_profiling_utils import load_
 from igf_airflow.utils.dag9_tenx_single_cell_immune_profiling_utils import task_branch_function
 from igf_airflow.utils.dag9_tenx_single_cell_immune_profiling_utils import upload_analysis_file_to_box
 from igf_airflow.utils.dag9_tenx_single_cell_immune_profiling_utils import convert_bam_to_cram_func
+from igf_airflow.utils.dag9_tenx_single_cell_immune_profiling_utils import run_picard_for_cellranger
 
 ## ARGS
 default_args = {
@@ -551,9 +552,19 @@ with dag:
       task_id='run_picard_alignment_summary',
       dag=dag,
       queue='hpc_4G',
-      python_callable=None,
-      params={'cellranger_xcom_key':'cellranger_output',
-              'cellranger_xcom_pull_task':'run_cellranger'})
+      python_callable=run_picard_for_cellranger,
+      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,
+              'load_metrics_to_cram':True,
+              'output_prefix':None,
+              'java_param':'-Xmx4g',
+              'picard_command':'CollectAlignmentSummaryMetrics',
+              'picard_option':{},
+              'analysis_files_xcom_key':'picard_alignment_summary',
+              'bam_files_xcom_key':None})
   ## PIPELINE
   decide_analysis_branch >> run_picard_alignment_summary
   ## TASK
@@ -562,7 +573,19 @@ with dag:
       task_id='run_picard_qual_summary',
       dag=dag,
       queue='hpc_4G',
-      python_callable=None)
+      python_callable=run_picard_for_cellranger,
+      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,
+              'load_metrics_to_cram':True,
+              'output_prefix':None,
+              'java_param':'-Xmx4g',
+              'picard_command':'QualityScoreDistribution',
+              'picard_option':{},
+              'analysis_files_xcom_key':'picard_qual_summary',
+              'bam_files_xcom_key':None})
   ## PIPELINE
   run_picard_alignment_summary >> run_picard_qual_summary
   ## TASK
@@ -571,7 +594,19 @@ with dag:
       task_id='run_picard_rna_summary',
       dag=dag,
       queue='hpc_4G',
-      python_callable=None)
+      python_callable=run_picard_for_cellranger,
+      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,
+              'load_metrics_to_cram':True,
+              'output_prefix':None,
+              'java_param':'-Xmx4g',
+              'picard_command':'CollectRnaSeqMetrics',
+              'picard_option':{},
+              'analysis_files_xcom_key':'picard_rna_summary',
+              'bam_files_xcom_key':None})
   ## PIPELINE
   run_picard_qual_summary >> run_picard_rna_summary
   ## TASK
@@ -580,10 +615,43 @@ with dag:
       task_id='run_picard_gc_summary',
       dag=dag,
       queue='hpc_4G',
-      python_callable=None)
+      python_callable=run_picard_for_cellranger,
+      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,
+              'load_metrics_to_cram':True,
+              'output_prefix':None,
+              'java_param':'-Xmx4g',
+              'picard_command':'CollectGcBiasMetrics',
+              'picard_option':{},
+              'analysis_files_xcom_key':'picard_gc_summary',
+              'bam_files_xcom_key':None})
   ## PIPELINE
   run_picard_rna_summary >> run_picard_gc_summary
   ## TASK
+  picard_base_dist_summary = \
+    PythonOperator(
+      task_id='run_picard_gc_summary',
+      dag=dag,
+      queue='hpc_4G',
+      python_callable=run_picard_for_cellranger,
+      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,
+              'load_metrics_to_cram':True,
+              'output_prefix':None,
+              'java_param':'-Xmx4g',
+              'picard_command':'CollectBaseDistributionByCycle',
+              'picard_option':{},
+              'analysis_files_xcom_key':'picard_base_summary',
+              'bam_files_xcom_key':None})
+  ## PIPELINE
+  run_picard_gc_summary >> picard_base_dist_summary
+  ## TASK
   run_samtools_stats = \
     PythonOperator(
       task_id='run_samtools_stats',