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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_Project: Change the name of some directory to make it easy to be read #49

Open lxwgcool opened 2 years ago

lxwgcool commented 2 years ago

Currently, there are a lot of folder named by date, which is not good to be managed (since we may submit jobs several times due to the cluster error).

We need to use the unique keywords to separate these folder rather than simply using date.

lxwgcool commented 2 years ago

1: global_config_bash.rc (1) Add three different names for different Log Types, including LOGTypeCoverage, LOGTypePreQC and LOGTypeRecaliBAM.

2: pre_calling_wgsqc_single.sh (1) Output some useful directory path in log file for debug

3: recalibrate_bam.sh (1) Output some useful directory path in log file for debug

4: step5_2_generate_coverage_report_batch.sh step5_generate_coverage_reportbatch.sh (1) Use "${LOGTypeCoverage}${strKTName}" to name the log folder

5: step6_2_generating_pre_calling_qc_report_batch.sh step6_generate_pre_calling_qc_reportbatch.sh (1) Use "${LOGTypePreQC}${strKTName}" to name the log folder

6: step8_sync_and_recalibratebam.sh (1) Use "${LOGTypeRecaliBAM}${strKTName}" to name the log folder to save recalibrate log file (2) Use "InQueue" subfolder to save the file FLG_INQUEUE

7: BackupCovid2ndPipelineResults.py (1) Use std_input to replace lowinput

8: MergeSubject.py (1) Increase the mem requirement