#run_irma.py
- irma_runner()
- Calls run_irma, move_results, sample_metrics from helper file
- Require Dictionary to paths, and path to resources folder, and iram output dir
- Creates json file to store assembly metrics, coverage and depth
#run_irma_helper.py
-
run_irma()
- Runs IRMA
- IRAM package located in resources folder
-
move_results()
- Moves IRMA results from Influenza Pipeline Directory to result location from user defined pipeline_resources.json file
-
sample_metrics()
- Uses samtools coverage tool to calculate depth and coverage on each protein segment produced by IRMA