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WF_1_freyja.md

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Workflow 1 Script

Annoates genome and Multilocus sequence typing


WF_1_freyja.py

  • run_script_nextflow()

    • Calls remove_bad_samples to remove samples with 0 or no coverage
    • Runs wasteWater.nf main process to run freyja

  • remove_bad_samples()

    • Loops through samples and removes samples with 0 or no coverage

wasteWater.nf

  • workflow()

    • Runs freyja to create variant files
    • Takes output and then runs freyja demix process

  • workflow final_step()

    • Runs freyja to create a aggregate demix file
    • Uses the aggregated file to create graph