Receive samples that have already done QC, CG does no RC

[annaengstrom]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: Different steps?
Protocol: And here!
Step: Here to!

Description: Some customers want to submit samples where we do no QC in RC, they want to send this information via the order. The workflow for TGA need to be updated so that we can get information from the order.

[pbiology]

Would be good to do for both TGA and WGS.

[Karl-Svard]

Summary of steps needed to be taken on the lims side:

• Add new boolean sample UDF called "Skip Reception Control QC" or "Skip Initial QC"
• Add this new UDF to the queue view of the Reception control steps of the TGA and WGS workflows
• In aggregate steps, either update the current EPPs to also fetch info from the sample level, or create a new separate one. Important here is to add the possibility to overwrite the info from the sample if we would feel like doing our own QC.
• Add new UDF to Arnold.

[Karl-Svard]

LIMS steps are completed

Added new sample UDFs

• Skip Reception Control QC, bool
• Concentration (ng/ul), numeric

Both these are set by cg according to the info in the connected order.

Added Skip Reception Control QC to relevant steps

For now, only steps from the workflow TWIST v8 have been updated. But you can easily add it to several ones in the future if requested.

Reception Control TWIST, Processing TWIST v3

• Queue
• Ice Bucket
• Record Details

Tapestation Reception Control TWIST, Initial QC TWIST v3

• Queue
• Ice Bucket
• Record Details

Qubit QC (DNA) TWIST, Initial QC TWIST v3

• Queue
• Ice Bucket

Quantit QC (DNA) TWIST, Initial QC TWIST v3

• Queue
• Ice Bucket

Aggregate QC (DNA) TWIST, Initial QC TWIST v3

• Queue
• Ice Bucket
• Record Details

Needed to update some EPPs

• cg_lims/EPPs/udf/calculate/calculate_amount_ng.py
• cg_lims/EPPs/udf/copy/sample_to_artifact.py

See the PR for further info:
#470

New automations

• Copy Customer Volume and Concentration, activated upon entry to the Aggregate QC (DNA) TWIST step. Will copy customer concentration (Concentration (ng/ul)) and volume (Volume (ul)) from the sample.
• Calculate Amount (Aggregate QC), calculates the amount (ng) based on the concentration and volumes set on the input artifacts. Was also added to the Aggregate QC (DNA) TWIST step.

Modified automations

Skipping Qubit/Quantit means we need to calculate the sample amount in the Aggregate QC step. This required a change to the current code, and thus the CLI command is slightly different. The flag -m is now a requirement for using the script in steps where UDFs are saved on measurement artifacts. The following automations were appended with this flag:

• Calculate Amount
• 2. Calculate Amount
• Prehyb QC - Calc Amount and Assign QC Flag

[Karl-Svard]

Update 2024-03-08

After feedback on the current implementation, we have instead decided to merge Copy Customer Volume and Concentration into 1. Aggregate QC Flags and Copy Fields. This is to minimize the amounts of different procedures needed to process both regular samples and those that have skipped RC QC.

New Automation created, "1. Aggregate QC Flags and Copy Fields or Customer Values":

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy sample-to-artifact -sudf 'Concentration (ng/ul)' -audf 'Concentration' -i --ignore-fail && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy sample-to-artifact -sudf 'Volume (uL)' -audf 'Volume (ul)' -i --ignore-fail && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy aggregate-qc-and-copy-fields"

Added to Aggregate QC (DNA) TWIST v2