WF_Phoenix.md

Phoenix Workflow Script

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Wrapper Script to Run Phoenix

WF_1_Launcher.py

• WF_1_Launch_Phoenix

  • Creates output folder
  • Creates samplesheet needed for Phoenix
  • Runs Phoenix

• WF_2_PushDB_phoenix

  • Calls Phoenix_create_dict to format Phoenix output into DICT format for DB push
  • Pushes results to SQL DB

WF_1_helper.py

• sample_organizer()

  • Creates samples sheet for Phoenix
  • Returns sample IDs for down stream use

• run_phoenix_pipeline()

  • Runs Phoenix

• Phoenix_create_dict()

  • Creates dictionaries for Phoneix output files
  • Calls parse_phoenix_AMR to create AMR_gene dict

• parse_phoenix_AMR()

  • Create a dictionary of AMR genes for a given sample