Clinical-Genomics/cg_lims issues and pull requests

#364 - New data from lims

Issue - State: closed - Opened by EmiliaRegazzoni over 1 year ago - 2 comments

#363 - Show "Source" in Initial QC TWIST Quant-it queue

Issue - State: closed - Opened by amandaraud over 1 year ago - 2 comments
Labels: Effort: Small, good first issue

#362 - Add RC method document in TGA Aliquotation

Issue - State: closed - Opened by amandaraud over 1 year ago - 2 comments
Labels: Effort: Small, good first issue

#361 - Add H2O lot number in a lims step

Issue - State: open - Opened by EmiliaRegazzoni over 1 year ago - 2 comments
Labels: Effort: Small, good first issue, Urgency: Small, Gain: Small

#360 - Change to a universal set of PCR plate thresholds

Pull Request - State: closed - Opened by Karl-Svard over 1 year ago

#359 - Add new template for manual backup verifications

Pull Request - State: closed - Opened by Karl-Svard over 1 year ago

#358 - Edit Library Preparation Method choices in WGS aliquotation

Issue - State: closed - Opened by amandaraud over 1 year ago - 1 comment
Labels: Effort: Small, good first issue, Urgency: Small

#357 - Broken EPPs caused by an ongoing issue with cg-prod-services, 2023-03-29, 2023-04-03

Issue - State: closed - Opened by Karl-Svard over 1 year ago - 6 comments

#356 - Change QC pass limit for cfDNA samples for EPP "Calculate Amounts" in TWIST v7

Issue - State: closed - Opened by idalindegaard over 1 year ago - 3 comments
Labels: Urgency: Medium, Gain: Large

#355 - RNA RC allowed to proceed without pressing all blue buttons EPPs

Issue - State: closed - Opened by EmiliaRegazzoni over 1 year ago - 1 comment
Labels: bug

#354 - TWIST QC RC Quantit new info column

Issue - State: open - Opened by EmiliaRegazzoni over 1 year ago
Labels: Effort: Medium, Urgency: Small, Gain: Small

#353 - cfDNA update for make_kapa_csv.py

Pull Request - State: closed - Opened by Karl-Svard over 1 year ago - 1 comment

#352 - Sort columns in the file generated by the script "Hamilton Quantit plate"

Issue - State: open - Opened by Manoj-Bandaru over 1 year ago
Labels: Effort: Small, Urgency: Medium, Gain: Small

#351 - Adjust PCR cycle plate distribution according to sample source

Issue - State: closed - Opened by VasKyriak over 1 year ago - 5 comments

#350 - Add nuclease free H2O to step in TGA

Issue - State: closed - Opened by EmiliaRegazzoni over 1 year ago - 1 comment

#349 - Add a column in Genotyping WF to visualised the remaining volumes for the samples

Issue - State: open - Opened by MarcelaGa over 1 year ago - 4 comments
Labels: Effort: Medium, Urgency: Medium, Gain: Medium

#348 - RC WGS/TGA: Update script that calculates amount needed to avoid negative values

Issue - State: closed - Opened by annaengstrom over 1 year ago - 4 comments
Labels: Urgency: Small

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

Issue - State: closed - Opened by annaengstrom over 1 year ago - 4 comments
Labels: Urgency: Large, Gain: Large

#346 - Add Hamilton Normalisation in micro prep

Issue - State: closed - Opened by FayKanellidou almost 2 years ago - 5 comments
Labels: Effort: Small, Urgency: Large, Gain: Medium

#345 - Add new sample UDF: "Number of sequencing runs" (or similar)

Issue - State: open - Opened by Karl-Svard almost 2 years ago

#344 - Update of 96 well placement map EPP

Pull Request - State: closed - Opened by Karl-Svard almost 2 years ago - 1 comment

#343 - Update Kapa Debug script with new method document

Issue - State: open - Opened by annaengstrom almost 2 years ago

#342 - Pooling map/placement map in pooling for hybridisation sorted in "well" order for ease of use

Issue - State: open - Opened by EmiliaRegazzoni almost 2 years ago
Labels: Urgency: Small, Gain: Medium

#341 - Bait set version missing in Development workflow

Issue - State: closed - Opened by annaengstrom almost 2 years ago - 2 comments

#340 - Simplify the process of changing well location on submitted samples

Issue - State: open - Opened by Karl-Svard almost 2 years ago

#339 - Change default to quantit

Issue - State: closed - Opened by EmiliaRegazzoni almost 2 years ago - 1 comment

#338 - Update LIMS stage

Issue - State: closed - Opened by Karl-Svard about 2 years ago - 1 comment

#337 - Change SMTP configuration to use new KTH accounts

Issue - State: closed - Opened by Karl-Svard about 2 years ago - 2 comments

#336 - Add new one time script to fetch samples of certain UDF values

Pull Request - State: closed - Opened by Karl-Svard about 2 years ago

#335 - Add UDF option in Lims step for Twist v7

Issue - State: closed - Opened by FayKanellidou about 2 years ago - 2 comments
Labels: Effort: Small, Gain: Small

#334 - Small adjustments for reception control in lims

Issue - State: closed - Opened by EmiliaRegazzoni about 2 years ago - 13 comments

#333 - Add new Atlas Tapestation doc in LIMS workflows.

Issue - State: closed - Opened by VasKyriak about 2 years ago - 1 comment
Labels: Effort: Small, Gain: Large

#332 - Make Lims able to process multiple plates in QC

Issue - State: closed - Opened by FayKanellidou about 2 years ago - 5 comments
Labels: Effort: Large, Urgency: Medium, Gain: Medium

#331 - Add qPCR in the copy task menu of the Aggregate QC (Library Validation) (Dev)

Issue - State: closed - Opened by MariaSalli about 2 years ago - 1 comment

#330 - Add Hamilton Udf in Lims Aliquotation step for WGS

Issue - State: closed - Opened by FayKanellidou about 2 years ago - 1 comment
Labels: Effort: Small

#329 - Update CODEOWNERS

Pull Request - State: closed - Opened by Karl-Svard about 2 years ago

#328 - More detailed error description

Pull Request - State: open - Opened by RasmusBurge-CG about 2 years ago - 1 comment

#327 - New EPPs and fixes needed for Quantit on hamilton

Pull Request - State: closed - Opened by Karl-Svard about 2 years ago - 2 comments

#326 - Add measurement level

Pull Request - State: closed - Opened by RasmusBurge-CG about 2 years ago - 1 comment

#325 - Add support for tagmentation in RB buffer calc

Pull Request - State: closed - Opened by Karl-Svard about 2 years ago - 2 comments

#324 - make the barcodes shorter and sort them

Pull Request - State: closed - Opened by RasmusBurge-CG about 2 years ago - 1 comment

#323 - Check that no defaults are set for old AM Method udfs

Issue - State: closed - Opened by Karl-Svard about 2 years ago - 2 comments

#322 - Change accepted amount values in script "Calculate RB volume"

Issue - State: closed - Opened by idalindegaard about 2 years ago - 2 comments
Labels: help wanted

#321 - New Return Samples WF

Issue - State: closed - Opened by RasmusBurge-CG about 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Small, Gain: Large

#320 - New plate reader EPP

Pull Request - State: closed - Opened by RasmusBurge-CG about 2 years ago

#319 - New workflow "WGS PCR-Free Tagmentation"

Issue - State: closed - Opened by RasmusBurge-CG about 2 years ago - 2 comments
Labels: Effort: Large, Gain: Large

#318 - Add in Lims Quantit and Tapestation plate preparation script for Hamilton

Issue - State: closed - Opened by FayKanellidou about 2 years ago - 2 comments
Labels: Urgency: Medium, Gain: Medium

#317 - Add Barcodes at Clinical Genomics to RC TGA

Issue - State: closed - Opened by RasmusBurge-CG about 2 years ago - 1 comment
Labels: Atlas

#316 - Add Barcodes at Clinical Genomics to RC WGS

Issue - State: closed - Opened by RasmusBurge-CG about 2 years ago - 1 comment
Labels: Atlas

#315 - Add Atlas link for manual KAPA in lims

Issue - State: closed - Opened by EmiliaRegazzoni about 2 years ago - 4 comments
Labels: Atlas

#314 - Adds script to assigned barcodes

Pull Request - State: closed - Opened by RasmusBurge-CG about 2 years ago - 2 comments

#313 - Adds script that generates barcodes

Pull Request - State: closed - Opened by RasmusBurge-CG about 2 years ago

#312 - Add method instructions to Atlas Illumina_COVIDseq_on_Hamilton

Issue - State: closed - Opened by MarcelaGa about 2 years ago - 6 comments
Labels: Atlas

#311 - Show TAT in delivery

Issue - State: closed - Opened by moahaegglund over 2 years ago - 5 comments

#310 - Make a "Case Cancelled Check" script

Issue - State: open - Opened by RasmusBurge-CG over 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Medium, Gain: Medium

#309 - Users are able to move to next step without saving "Level of Multiplexing" to sample level.

Issue - State: closed - Opened by RasmusBurge-CG over 2 years ago - 2 comments
Labels: Effort: Small, bug, Urgency: Small, Gain: Medium

#308 - calculate volume script in TGA workflow for normalisation

Issue - State: open - Opened by EmiliaRegazzoni over 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Medium, Gain: Large

#307 - Transfer 1830 to Atlas

Issue - State: closed - Opened by idalindegaard over 2 years ago - 3 comments
Labels: Atlas

#306 - Quantit result file upload in WGS RC

Issue - State: closed - Opened by ceciliamattssonscilifelab over 2 years ago - 3 comments

#305 - Minor changes to lucigen

Issue - State: closed - Opened by RasmusBurge-CG over 2 years ago - 1 comment
Labels: Effort: Small, Urgency: Small, Gain: Small

#304 - Transfer qPCR dilution EPP

Pull Request - State: closed - Opened by Karl-Svard over 2 years ago - 7 comments

#303 - Set "Primer" for all sars-cov-2 samples processed so far

Issue - State: closed - Opened by henningonsbring over 2 years ago - 2 comments

#302 - Qubit and Quant-iT updates (Atlas move)

Issue - State: closed - Opened by ceciliamattssonscilifelab over 2 years ago - 6 comments
Labels: Atlas

#301 - Transfer 2234 to Atlas

Issue - State: closed - Opened by RasmusBurge-CG over 2 years ago - 6 comments
Labels: Atlas

#300 - Small bug in Micro workflow in this step "CG002 - Microbial Library Prep (Nextera)". No EPP Log and the first file is a placement map. Need to change the output of placement map file to second placeholder.

Issue - State: closed - Opened by cesve over 2 years ago - 6 comments
Labels: Effort: Small

GitHub / Clinical-Genomics/cg_lims issues and pull requests