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Workflow 1 Script


Run IRMA: Iterative Refinement Meta-Assembler


#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