LIMS improvements for RC TGA

[AbiDalby]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: TWIST v8
Protocol: Pre Processing TWIST v3, Initial QC TWIST v3
Step: Reception Control TWIST, Aggregate QC (DNA) TWIST

Description:

Suggestion 1: Change "Atlas Method Document" to trigger automatically. Some other scripts could potentially be combined to allow this EPP to be run automatically on exit from either the step or record details.

Suggestions 2+3: Similarly to suggested changes in RC WGS, altering the script of "Get Barcode File & Set Barcode udf" to generate an excel file in the .xlsx format instead of .csv for compatibility to the Brady programme. In the queue interface, the RC TGA person scans the customer barcode on the tube and places the corresponding Brady printed barcode onto the tube for handling in Hamilton. The udfs needed here are "Sample Name" and "LIMS ID". Other udfs could be removed to keep only a few in this interface for ease for the user.

Suggestion 4: Investigate possibility of automatic replies from LIMS to FreshDesk/customer with failed samples after RC. Relevant for RC WGS too. Possibly too large to be included in this issue and needs its own separate issue and collaboration with IT/Freshdesk responsible.

Suggestion 5: Link to issue 612 regarding improvements in normalisation to be able to normalise samples for enzymatic fragmentation and cfDNA (direct to KAPA library prep step) in the same lims step. Generating a single Hamilton file that differentiates the differing total volumes (30uL enzymatic frag, 50uL KAPA library prep).

[idalindegaard]

RC related issues:
#435 (also for WGS): Concerning Aliquot samples for enzymatic fragmentation TWIST - FIXED
#466: Initial QC - Quantit, Qubit and Aggregate steps. The part of the issue mentioning the changes needed for the aliquotation step is already fixed

[idalindegaard]

Fixed suggestion 1 (although it's not automatic upon exit):

New EPP: Set date, missing reads and Atlas Method Document

bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy process-to-sample -sudf 'Received at' -pudf 'date arrived at clinical genomics' && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set set-reads-missing-on-new-samples && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set method-document -pru 'Library Preparation Method'  -pru 'Library Preparation Method 1' -pru 'Library Preparation Method 2' -pru 'Supporting Procedure Document' -pru 'Supporting Procedure Document 1' -pru 'Supporting Procedure Document 2' -pru 'Equipment Document' -pru 'Equipment Document 1' -pru 'Equipment Document 2' -pru 'Sequencing Method' -pru 'Library preparation method'"