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NCI-CGR / IlluminaSequencingAnalysis

All Illumina Sequencing Related project from Xin will be recorded in this repo
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COVID_Auto_Framework: Add Email Notification #46

Open lxwgcool opened 2 years ago

lxwgcool commented 2 years ago

Add email notification into the COVID Auto Framework.

It contains many useful info.

Please check the example below:

============ std_input_01_200_keytable ============ 

Good News              : The keytable std_input_01_200_keytable IS ALL SET (COVID 2nd Analysis Pipeline) 

Total Number of Subject: 200

======== Please Check the Results Below (Biowulf) ========  

Re-calibrated BAM File Path ------ : /data/COVID_WGS/lix33/Test/2ndpipeline/Data/BAM_reformatted/BAM_recalibrated/WGS

Coverage Report Path ------------- : /data/COVID_WGS/lix33/Test/2ndpipeline/Data/secondary_buf/coverage_report/{contain keywords coverage}

Pre-calling QC Report Path ------- : /data/COVID_WGS/lix33/Test/2ndpipeline/Data/secondary_buf/coverage_report/{contain keywords pre-calling QC}

BAM Contamination Check Report Path: /data/COVID_WGS/lix33/Test/2ndpipeline/Build/processed/build_CGR_std_input_01_200_keytable/Report

======== Some Useful Directories are also listed below (Biowulf) ========  

Build Dir  -------------------: /data/COVID_WGS/lix33/Test/2ndpipeline/Build/processed/build_CGR_std_input_01_200_keytable

Original BAM Dir (after Merge): /data/COVID_WGS/lix33/Test/2ndpipeline/Data/BAM_reformatted/ BAM_original/WGS

Retrieved Flowcell (From S3)  : /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/std_input_01_200_keytable

Flag Dir  ------------------- : /data/COVID_WGS/lix33/Test/2ndpipeline/Data/BAM_reformatted/BAM_recalibrated/Flag

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/std_input_01_200_keytable/Flag

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/lix33/Test/2ndpipeline/Build/processed/build_CGR_std_input_01_200_keytable/Flag

Log Dir:                      : /data/COVID_WGS/lix33/Test/2ndpipeline/Data/secondary_buf/cluster_job_logs

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/lix33/Test/2ndpipeline/Build/tmp/std_input_01_200_keytable/Log

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/UpstreamAnalysis/PostPrimaryRun/Data/BAM/Batch/std_input_01_200_keytable/Flag

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/lix33/Test/2ndpipeline/Build/tmp/std_input_01_200_keytable/Script

      >>>>>>>>>>>>>>>>>>>>>>> : /data/COVID_WGS/lix33/Test/2ndpipeline/Build/processed/build_CGR_std_input_01_200_keytable/Log

Report Dir -------------------: /data/COVID_WGS/lix33/Test/2ndpipeline/Data/secondary_buf/coverage_report

Pre-QC Tmp Result Dir --------: /data/COVID_WGS/lix33/Test/2ndpipeline/Data/secondary_buf/PRE_QC

BAM Contamination Check Dir   : /data/COVID_WGS/lix33/Test/2ndpipeline/Build/processed/build_CGR_std_input_01_200_keytable/Report,Log,Flag

Mimic Manifest Dir -----------: /data/COVID_WGS/lix33/Test/2ndpipeline/Build/tmp/std_input_01_200_keytable/Manifest_Mimic.csv
lxwgcool commented 2 years ago

Attach all three different types of files in email.