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@@ -528,6 +528,50 @@ with dag:
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'collection_type':'ANALYSIS_CRAM',
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'collection_table':'sample',
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'cram_files_xcom_key':'cram_files'})
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+ ## PIPELINE
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+ decide_analysis_branch >> convert_cellranger_bam_to_cram
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+ ## TASK
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+ generate_cell_sorted_bam = \
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+ DummyOperator(
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+ task_id='generate_cell_sorted_bam',
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+ dag=dag)
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+ run_velocyto = \
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+ DummyOperator(
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+ task_id='run_velocyto',
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+ dag=dag)
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+ run_scvelo_for_sc_5p = \
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+ DummyOperator(
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+ task_id='run_scvelo_for_sc_5p',
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+ dag=dag)
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+ load_loom_file_to_rds = \
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+ DummyOperator(
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+ task_id='load_loom_file_to_rds',
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+ dag=dag)
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+ upload_loom_file_to_irods = \
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+ DummyOperator(
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+ task_id='upload_loom_file_to_irods',
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+ dag=dag)
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+ load_scvelo_report_to_rds = \
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+ DummyOperator(
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+ task_id='load_scvelo_report_to_rds',
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+ dag=dag)
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+ upload_scvelo_report_to_ftp = \
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+ DummyOperator(
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+ task_id='upload_scvelo_report_to_ftp',
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+ dag=dag)
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+ upload_scvelo_report_to_box = \
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+ DummyOperator(
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+ task_id='upload_scvelo_report_to_box',
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+ dag=dag)
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+ ## PIPELINE
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+ convert_cellranger_bam_to_cram >> generate_cell_sorted_bam
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+ generate_cell_sorted_bam >> run_velocyto
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+ run_velocyto >> run_scvelo_for_sc_5p
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+ run_velocyto >> load_loom_file_to_rds
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+ load_loom_file_to_rds >> upload_loom_file_to_irods
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+ run_scvelo_for_sc_5p >> load_scvelo_report_to_rds
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+ load_scvelo_report_to_rds >> upload_scvelo_report_to_ftp
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+ load_scvelo_report_to_rds >> upload_scvelo_report_to_box
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## TASK
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copy_bam_for_parallel_runs = \
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BranchPythonOperator(
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@@ -557,8 +601,8 @@ with dag:
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'collection_name_task':'load_cellranger_result_to_db',
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'analysis_name':'cellranger_multi'})
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## PIPELINE
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- decide_analysis_branch >> convert_cellranger_bam_to_cram
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- convert_cellranger_bam_to_cram >> copy_bam_for_parallel_runs # we need to load metrics to cram
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+ #convert_cellranger_bam_to_cram >> copy_bam_for_parallel_runs # we need to load metrics to cram
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+ generate_cell_sorted_bam >> copy_bam_for_parallel_runs
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convert_cellranger_bam_to_cram >> upload_cram_to_irods
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## TASK
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run_picard_alignment_summary = \
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