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QC Configuration File

Overview

The QC configuration file is in the TOML (Tom's Obvious, Minimal Language) format. It defines the distribution of Quality Control (QC) and specimen samples within a multiwell plate. This file is structured into several key sections, each tailored for different aspects of the plate layout.

Example

[QC]
# should first well(s) be a QC round?
start_with_QC_round = true
# how many non-QC samples to analyze until we start a round of QC samples? 
run_QC_after_n_specimens = 11 

[QC.names] 
# Describes the key names and descriptions of the QC samples used.
EC = "EC: External_Control_(matrix)"
PB = "PB: Paper_Blank"
PO = "PO: Pooled_specimens"

[QC.patterns]
# start = ["EC", "PB"]
then_alternating = [["EC", "PB"], ["EC", "PO"]]

Sections

[QC] Section

This section includes general settings for the QC layout.

  • start_with_QC_round (boolean): Determines whether the first wells should contain QC samples. Set to true to start with a QC round; false otherwise.
  • run_QC_after_n_specimens (integer): The number of non-QC (specimen) samples to analyze before starting a new round of QC samples.

[QC.names] Section

Describes the key names and descriptions of the QC samples used. For example:

  • EC = "EC: External_Control_(matrix)"
  • PB = "PB: Paper_Blank"
  • PO = "PO: Pooled_specimens"

[QC.patterns] Section

Defines the hierarchy and patterns for QC sample placement throughout the plate.

Hierarchy of Patterns:

  • Specific Round Patterns: Highest priority. Specific instructions for individual rounds (e.g., round_3).
  • Start/End Patterns: Determine patterns for the beginning (start) and end (end) of the plate.
  • Repeat Pattern: Specifies a pattern (repeat_pattern) to be repeated a certain number of times.
  • Alternating Patterns: Defines alternating patterns (then_alternating) that provide a general structure.
  • Every N Rounds Patterns: Lowest priority. General patterns applied every N rounds (e.g., every_4_rounds).

Pattern Examples:

  • round_3 = ["EC", "PO", "PB"]: Specific pattern for round 3.
  • every_4_rounds = ["EC", "PB"]: Pattern applied every 4 rounds.
  • start = ["EC", "PB"]: Pattern for the start of the plate.
  • then_alternating = [["PB", "PO"], ["EC", "PO"]]: Alternating patterns.
  • end = ["PB"]: Pattern for the end of the plate.
  • repeat_pattern = { pattern = ["EC", "PB"], times = 3 }: Repeats the specified pattern 3 times.

Note

Ensure that the sum of all patterns does not exceed the plate capacity and that each pattern is configured correctly to avoid layout errors.