EPP Queue Samples for sequencing (with variations) moves samples regardless of QC flags and choice to leave samples in QC protocol

[idalindegaard]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: All prep workflows
Protocol: Last protocols of all prep workflows
Step: Last step of all prep workflows

Description:

When MGG queued samples from LIMS workflow WGS PCR free v6 to Queue Samples for Sequencing v2 we discovered that samples that had a red QC flag and were supposed to be left in the QC protocol had both been left there and sent to the next step. Discussed with KSV and ARW and we realized that the Queue samples for sequencing EPP is placed when exiting the Record details step. After Record details at the end of a QC protocol there's always an option to choose to complete or leave the sample(s) in the protocol. With this setup as we have now, we will always send the samples to the next step regardless of what option we choose.

Would be necessary to change the script and/or move it to the very last step in the protocol, in accordance with the chosen option for what to do with the samples

[Karl-Svard]

The API statuses are unfortunately a bit shaky, as summarised in the following sheet:

https://docs.google.com/spreadsheets/d/1TFNlH7eDIHZCM495gUWraJl1oVNZaXL_ej0DavyOV7k/edit#gid=0

You could add some checks that only queue samples that have a status of "COMPLETED" and not those that also have "QUEUED". But the risk of samples being incorrectly sent for sequencing (or lost) seems quite high. It would need to be properly tested before being implemented in production.

A safer option would be to have some sort of check box for either queueing or not queueing samples for sequencing. But this would result in more manual work for the user.