LIMS improvements for RC WGS

[AbiDalby]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: WGS PCR free v6 Protocol: Initial QC wgs v4, TruSeq DNA PCR-free Library Prep Step: CG002 - Reception Control, Aliquot Samples for Covaris

Description:

Suggestions for improvments in LIMS to help RC WGS from CM.

Suggestion 1: For the CG002 - Reception Control step (when selecting which samples to add to the Ice Bucket), often barcodes for Sarstedt tubes are added. Each sample tube is manually scanned using the customers own barcodes to identify the tube before we place our own barcodes on top.

We compare the "LIMS ID" to the "Sample Name" to ensure no sample mix up. Many columns are present in this interface and the RC person needs to manually drag the columns to make the others small enough to be able to see the Sample Name and LIMS ID. Suggestion to remove many other columns from this view as they are not necesary so the Sample Name and LIMS ID columns are more visible. This would also be relevant for RC TGA

Suggestion 2: Combine "Atlas Method Document" and "Set date and missing reads" together. Atlas Method Document may be able to be triggered "Automatic upon exit" at "Record Details" and is probably better kept separate since this script is used in almost all master steps and workflows, and set date and missing reads is also used in several different workflows and steps.

Suggestion 3: "Generate Barcode File & Set Barcode" could this script be changed to generate the file as an .xlsx file instead of .csv. At the moment the RC person opens the .csv file on the Brady printer computer and re-saves as an .xlsx file in order to import into the Brady programme. This would also be relevant for RC TGA.

Suggestion 4: In the Place Samples screen in the "Aliquot Samples for Covaris" change the default fill containers by pattern to fill containers by column. This is due to some customers delivering samples in columns 1 and 7 in the same plate. Currently the RC WGS person has to manually change this setting. Also, some columns in this interface could be removed as the RC WGS person is most interested in the udfs "Priority" and "Sequencing Analysis". All small changes that can help speed up the RC process.

[idalindegaard]

https://docs.google.com/presentation/d/1NU85qSvmyfATijm8V2OuWAPOd8unGDvfpE1tAxYz88M/edit#slide=id.p

[idalindegaard]

RC related issues, both concerning step Aliquot Samples for Covaris: #435, #348

[idalindegaard]

Suggestion 1 fixed together with CM. Suggestion 4 also fixed.

[idalindegaard]

For Suggestion 2 there's a new EPP called "Check Missing Sample UDFs & Atlas Method Document" that is running automatically upon exit from Record details, merging two already existing EPPs into one.

bash -c -l conda activate cg_lims && 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' && bash -c "/home/glsai/miniconda3/envs/epp_master/bin/check_missing_sample_udfs.py -p {processLuid}"

A quick test in stage showed that the EPP works without errors

[idalindegaard]

Another WGS RC related issue #471, but applies to all steps in all workflows that perform Hamilton normalisation and pooling