Changes to "Set QC" scripts from clinical EPPs

[AbiDalby]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: Several
Protocol: QC protocols
Step: Quantit, Qubit, Aggregation, Tapestation, Femto Pulse QC steps

Description:

Lab Logic Toolkit has been used for many QC EPPs, although it sets the QC flags correctly, it does not pop up as a warning message to the LIMS user that a sample (or several) failed QC and thus received a red flag.

Since the script was successfully run, it is indicated by a green message which can be misleading to the LIMS user and could be misinterpreted as all samples passed QC.

For ease to the LIMS user, we would like all QC scripts to indicate how many and which samples failed QC.

Many older workflows utilise the clinical EPPs scripts: set_qc.py and setQC.py or they have a script in cg_lims that combines for example calculate molar concentration and set QC. These older scripts found in clinical_EPPs are able to define which samples failed QC and receive a red flag.

This update could be implemented at the same time as moving the scripts from clinical_EPPs to cg_lims repo which are ongoing issues here:

• set_qc
• setQC