Comments (1)
added the submodule, next need to add integration
maybe split the 'run.py' script into separate 'start sns' and 'analyze sns' scripts
also consider single script with multiple arg subcommands with argparse or similar
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Related Issues (20)
- Need program framework dependency graph HOT 1
- Need backup email notification in case of email send failure
- Need running tasks to kill their jobs on error HOT 4
- Email not going to inbox HOT 2
- Integrate QC checks in reports and program output
- Separate log file for each analysis, sample, and task
- Move log dir to parent directory HOT 2
- Move binary configs to parent directory
- MuTect2 split jobs task HOT 1
- refactor analysis report to utilize sns analysis steps HOT 1
- refactor sns_task submodule names
- mutt does not work on cluster nodes HOT 2
- need mini targets & probes for testing HOT 1
- need small datasets for testing
- SnsWESAnalysisOutput class not compatible with other sns pipeline outputs HOT 2
- refactor 'task_lists' into 'pipelines'
- need to fork snsxt into more generic framework
- logger filehandler paths getting printed repeatedly at end of analysis
- MuTect2_split printing tons of job IDs to email log
- sns jobs being caught and Job objects generated before log file is created
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