config_ucsf.yml

"protocol_name": "Promega N1/N2 assay on Pro machine"
"analysis_settings":
  "curve_model": pooled  # options: single, pooled, mixed
  "normalization_model": fixed  # options: spikein, rolling, fixed
  "fixed_norm_factors":
    "PL": 5000000000
    "ENC": 2000000000
    "SB": 2000000000
    "default": 5000000000  # TODO: verify
  "rolling_norm_divisors":
    "PL": 50
    "ENC": 50
    "SB": 100
  "min_passing_reps": 1
  "min_cq_conf": 0.7
  "sample_context_fold_change_threshold": 2.5
  "sample_base_context_fold_change_threshold": 2
  "sample_base_context_days_window": 2
  "sample_base_context_days_threshold": 5
  "control_days_for_rolling_avg": 7
  "min_control_days_for_rolling_avg": 1

"standard_curves":
  "PMMoV_N1":
    "curve_name": "legacy_std_curve"
    "slope": -3.713
    "intercept": 36.5
    "use_ln": False
    "reaction_vol_per_l": 1000000
  "Promega_N1":
    "curve_name": "legacy_std_curve"
    "slope": -3.493
    "intercept": 40.6
    "use_ln": False
    "reaction_vol_per_l": 1000000

"spikein_curves":
  "NA":
    "NA": "NA"

"input_files":
  "exclude_fname_pattern": "*_exclude.yml"
  "filename_pattern": "*_Results_*.*"
  "sheet_name": "Results"
  "date_created_key": "Analysis Date/Time"
  "metadata_separator": ": "
  "rows_to_skip": 24
  "well_key": "Well Position"
  "sample_key": "Sample"
  "target_key": "Target"
  "raw_cq_key": "Cq"
  "confidence_key": "Cq Confidence"
  "null_value": "Undetermined"
  "assays":
    - "assay_name": "Promega_SARS-CoV-2_N1"
      "targets":
        - "target_name": "Promega_N1"
          "ladder_prefix":
            - "Ladder_per_uL_"
        - "target_name": "PMMoV_N1"
          "is_fecal_control": true
          "ladder_prefix":
            - "Ladder_per_uL_"
    - "assay_name": "Promega_SARS-CoV-2_N2"
      "targets":
        - "target_name": "Promega_N2"
          "ladder_prefix":
            - "Ladder_per_uL_"
        - "target_name": "PMMoV_N2"
          "is_fecal_control": true
          "ladder_prefix":
            - "Ladder_per_uL_"
    - "assay_name": "Monkeypox"
      "targets":
        - "target_name": "MPX"
  "control_prefixes":
    - "neg"
    - "pos"
    - "control"
  "ladders":
    "ladder_bottom": 0.004
    "ladder_steps": 8
    "intercept_ladder_step": 3
    "regression_bottom_step": 3

"site_groups":
    - "site_group": "sandiego"
      "site_prefixes":
        - "PL"
        - "ENC"
        - "SB"
      "do_context_qc": true
      "site_locations":
        "PL": "PointLoma"
        "ENC": "Encina"
        "SB": "SouthBay"
      "filename_pattern": "{}_sewage_qPCR.csv"
    - "site_group": "ucsd"
      "site_prefixes":
        - "AS"
        - "ECEC"
        - "THN"
      "do_context_qc": false
    - "site_group": "ucsf"
      "site_prefixes":
        - "SEP"
        - "OSP"
        - "SFO"
      "do_context_qc": false
    - "site_group": "usd"
      "site_prefixes":
        - "USD"
      "do_context_qc": false

"output_files":
  "norm_conc_key": "Mean viral gene copies/L"
  "collection_date_key": "Sample_Date"
  output_assay:
    "assay_name": "Promega_SARS-CoV-2_N1"