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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: Several New features #47

Open lxwgcool opened 2 years ago

lxwgcool commented 2 years ago

New Feature: Run Pre-calling QC and BAM Contamination Check simutaniously

Details:

Since these two steps are not conflicted with each other, we can run them simutaniously.

lxwgcool commented 2 years ago

New Feature: Backup all three types of report into the specific folder

Details 1: Right now, we have three different types of report file, including coverage report, Pre-QC report and BAM Contamination Report. 2: They are located in different folder 3: It is necessary to backup them into the same folder to make people easy to find.

lxwgcool commented 2 years ago

Back up three types of report to UpStreamAnalysis PostPrimaryAnalysis Dir

1: step5_2_generate_coverage_report_batch.sh (1) Check if report folder in UpstreamAnalysis PostPrimaryRun is existed. (2) Check if the report file has been backed up. (3) Back up Coverage Report file

2: step6_2_generating_pre_calling_qc_report_batch.sh (1) Check if report folder in UpstreamAnalysis PostPrimaryRun is existed. (2) Check if the report file has been backed up. (3) Back up Pre-QC Report file

3: AutoFramework.py (1) Deliver 1 more argument to ContaminationCheck.py

4: ContaminationCheck.py (1) Add 1 more argument (Keytable Name). (2) Check if report folder in UpstreamAnalysis PostPrimaryRun is existed. (3) Check if the report file has been backed up. (4) Back up Sum-BAM-Contamination Report file