Y24-320 - [BUG] For the new PiMmS_TruSeq_adapters_v1 libraries or pools should be treated as untagged but the the hidden sample sheet bheviour is not working as expected for the new style sample sheets

[stevieing]

Describe the bug

Thanks for making Live in production. In my haste, I've just realised that I performed UAT as if it is a normal Tag set. Previously, we had the functionality with the TruSeq_CD_i7_i5 tag group that if selected the libraries or pools would be treated as if they are untagged, the biosample name would be a concatenation of all the samples in the pool - the customer deplexes these samples as the tags are asymmetric so unsupported in TRACTION. I think this may have 'broken' with the new csv format. Runs containing libraries with the TruSeq tag group now export a csv file that contains tagged libraries rather than treating them as untagged. The new PiMmS tag set should be treated the same way. I suspect that this is not a quick fix and I have some libraries to load using this tag group. However, I can manually edit the csv file to replicate the previous functionality for the 'Bio Sample Name' row so I can get the libraries sequenced (assuming this is not going to cause any major problems).
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[stevieing]

Incorrect sample sheet:
TRACTION-RUN-1504.csv

Correct sample sheet:
TRACTION-RUN-1504-edit.csv

[stevieing]

Investigation:

• TruSeq_CD_i7_i5_D0x_8mer - Sequel IIe - v12 - TRACTION-RUN-34.csv
• TruSeq_CD_i7_i5_D0x_8mer - Revio - v13 - TRACTION-RUN-35.csv
• PiMmS_TruSeq_adapters_v1 - Sequel IIe - v13 - TRACTION-RUN-36.csv
• PiMmS_TruSeq_adapters_v1 - Revio - v13 - TRACTION-RUN-37.csv

In summary:

• when the sample sheet behaviour is set to hidden the behaviour is correct for Sequel IIe.
• when sample behaviour is set to hidden the behaviour is correct for Sequel IIe.

[stevieing]

I have created a new story to refactor the code to make it easier to maintain #1443