Clinical-Genomics/cg_lims issues and pull requests

#558 - New library normalization script for Revio

Pull Request - State: open - Opened by idalindegaard 6 days ago - 1 comment

#557 - Remove "delivery format"

Issue - State: open - Opened by RasmusBurge-CG 16 days ago

#556 - Adjust express samples, based on priority, with more reads to sequence

Issue - State: open - Opened by idalindegaard 20 days ago - 4 comments

#555 - Add Arnold support to the new Watchmaker workflow

Issue - State: open - Opened by Karl-Svard 24 days ago
Labels: Arnold, Trending, On Hold

#554 - Set date and missing reads automatically upon exit of Record details for RC WGS and TGA

Issue - State: closed - Opened by idalindegaard 25 days ago - 2 comments

#553 - Simplify moving between steps in lims

Issue - State: open - Opened by EmiliaRegazzoni 27 days ago - 1 comment

#552 - Generalize make_pooling_map for other workflows than covid

Issue - State: open - Opened by idalindegaard about 1 month ago

#551 - Patch aliquot volumes EPP for 0 ul volumes

Pull Request - State: closed - Opened by Karl-Svard about 1 month ago - 7 comments

#550 - Add new trending tool for top-ups

Pull Request - State: closed - Opened by Karl-Svard about 1 month ago - 1 comment

#549 - add input flag to normalization script

Pull Request - State: closed - Opened by idalindegaard about 1 month ago

#548 - Align delivery formats to our current delivery options

Issue - State: closed - Opened by karlnyr about 1 month ago - 2 comments
Labels: Effort: Medium, Urgency: Medium, Gain: Large

#547 - Add low volume warning to aliquot volume EPP

Pull Request - State: closed - Opened by Karl-Svard about 1 month ago - 2 comments

#546 - Update Queue samples for sequencing configuration in several LIMS workflows

Issue - State: closed - Opened by idalindegaard about 1 month ago - 2 comments

#545 - Update Queue samples for sequencing EPP order when finishing the microbial workflow

Issue - State: closed - Opened by idalindegaard about 1 month ago - 2 comments

#544 - Enable permission to modify/add notes in completed steps

Issue - State: open - Opened by mariarevenikioti about 1 month ago - 2 comments

#543 - Feature Request: Add new trending tool for top-ups

Issue - State: closed - Opened by Karl-Svard about 2 months ago - 1 comment
Labels: enhancement, Trending

#542 - New index set added for old naming formats

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

#541 - Compliance to Atlas document Validation and verifications and suggestion for improvment to templates

Issue - State: closed - Opened by AnnaLeinfelt about 2 months ago - 4 comments

#540 - In issue template - corrected link to Atlas instructions

Pull Request - State: closed - Opened by AnnaLeinfelt about 2 months ago

#539 - New "Check required" EPP for the Aggregation step in SARS-CoV-2 v4 wf

Issue - State: closed - Opened by idalindegaard about 2 months ago - 2 comments

#538 - Patch index parsing

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

#537 - Merge index and sample duplication check in Define Run Format

Issue - State: open - Opened by Karl-Svard about 2 months ago - 1 comment

#536 - Watchmaker EPP updates

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

#535 - Add TWIST Hamilton UDF to Arnold

Pull Request - State: closed - Opened by Karl-Svard about 2 months ago - 1 comment

#534 - Generalize and rename buffer aliquotation script used in the Sample Placement step in several LIMS workflows

Pull Request - State: closed - Opened by idalindegaard 2 months ago - 1 comment

#533 - Update library normalization script to work with the new Watchmaker LIMS workflow

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

#532 - LIMS improvements for RC TGA

Issue - State: open - Opened by AbiDalby 2 months ago - 2 comments

#531 - Count NTC reads in sequencing QC check

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

#530 - LIMS improvements for RC WGS

Issue - State: open - Opened by AbiDalby 2 months ago - 5 comments

#529 - Re-design pool_normalization script to normalize other samples than just pools - and make "Total Volume (uL)" work on process level

Issue - State: closed - Opened by idalindegaard 2 months ago - 2 comments

#528 - Make script calculate_water generalized for different kinds of udfs

Issue - State: closed - Opened by idalindegaard 2 months ago - 2 comments

#527 - WGS reception control - Change criterias for QC flags

Issue - State: closed - Opened by ceciliamattssonscilifelab 2 months ago - 1 comment

#526 - change constants for minimum lane volume

Pull Request - State: closed - Opened by idalindegaard 2 months ago - 2 comments

#525 - Add QC checks for Average Size (bp) and % of Total in Tapestation steps TWIST v8

Issue - State: closed - Opened by idalindegaard 3 months ago - 3 comments
Labels: Gain: Medium

#524 - Always add reads for negative controls - NovaSeq X v1 WF

Issue - State: closed - Opened by karlnyr 3 months ago - 3 comments
Labels: Effort: Medium, enhancement, Urgency: Medium, Gain: Large

#523 - Add Standards with Hamilton Norm-pooling for Quantit

Issue - State: open - Opened by FayKanellidou 3 months ago
Labels: Urgency: Medium

#522 - Raise the minimum Adjusted Bulk Pool Volume (ul) in step Define Run Format and Calculate Volumes (NovaSeq X)

Issue - State: closed - Opened by idalindegaard 3 months ago - 2 comments
Labels: Gain: Medium, NovaSeq X

#521 - Have an index check confirmation in Define Run Format and Calculate Volumes (NovaSeq X)

Issue - State: open - Opened by idalindegaard 3 months ago
Labels: Effort: Small, enhancement

#520 - New Watchmaker WGS workflow

Issue - State: closed - Opened by idalindegaard 3 months ago - 3 comments
Labels: Effort: Medium, Gain: Large

#519 - Change ONT parser from JSON to HTML

Pull Request - State: closed - Opened by Karl-Svard 3 months ago - 1 comment

#518 - New PacBio Revio workflow in LIMS

Issue - State: open - Opened by idalindegaard 3 months ago
Labels: Gain: Large

#517 - Update CODEOWNERS file

Pull Request - State: closed - Opened by Karl-Svard 3 months ago

#516 - Update CODEOWNERS

Pull Request - State: closed - Opened by idalindegaard 4 months ago

#515 - New EPP Adjust missing reads for sequencing

Pull Request - State: closed - Opened by idalindegaard 4 months ago - 1 comment

#514 - New EPP to adjust the sequencing reads for samples in Define Run Format and Calculate Volumes (NovaSeq X)

Issue - State: closed - Opened by idalindegaard 4 months ago - 3 comments
Labels: Urgency: Medium, Gain: Large

#513 - Update "Missing Reads pool (M)" udf for single samples as well

Issue - State: open - Opened by idalindegaard 4 months ago

#512 - Make a combo automation for "Atlas Method Document" and "Check missing sample udfs and set Next Step Remove" in micro RC step

Issue - State: closed - Opened by idalindegaard 5 months ago - 1 comment

#511 - Update the micro workflow

Issue - State: closed - Opened by FayKanellidou 5 months ago - 2 comments

#510 - Automate inventory calculations by retrieving number of samples processed in relevant LIMS steps

Issue - State: open - Opened by idalindegaard 6 months ago

#509 - Merge Copy Concentration (nM) EPPs in step Define Run Format and Calculate Volumes (NovaSeq X)

Issue - State: open - Opened by idalindegaard 6 months ago - 1 comment

#508 - Verify that the sample UDF Passed Initial QC is set in all reception control steps

Issue - State: open - Opened by Karl-Svard 6 months ago

#507 - Patch qPCR error handling

Pull Request - State: closed - Opened by Karl-Svard 6 months ago

#506 - Remove the Bravo Shirin from lims steps

Issue - State: closed - Opened by FayKanellidou 6 months ago - 3 comments

#505 - Update flow cell file path in xml_to_udf.py

Pull Request - State: closed - Opened by Karl-Svard 6 months ago

#504 - The available volume for ONT sequencing reloads doesn't work with re-preps

Issue - State: open - Opened by Karl-Svard 6 months ago

#503 - Patch ONT reload amount EPP

Pull Request - State: closed - Opened by Karl-Svard 6 months ago

#502 - New "Set RIN QC" EPP to accept cust127 samples with RIN over 4

Issue - State: closed - Opened by idalindegaard 6 months ago - 3 comments

#501 - Addition of a drop down menu to select the index plate in micro library prep

Issue - State: closed - Opened by AbiDalby 6 months ago - 3 comments

#500 - Add new process udf for NA24385 prep control to arnold

Pull Request - State: closed - Opened by Karl-Svard 7 months ago

#499 - Add "Check required" EPP for Output Container Barcode in step Post-PCR bead purification v1 (wf Microbial WGS v7)

Issue - State: closed - Opened by idalindegaard 7 months ago

#498 - Improve sequencing planning and pooling, prio 1 project

Issue - State: closed - Opened by EmiliaRegazzoni 7 months ago - 4 comments

#497 - Automation of Rsquare values from Quantit file to LIMS

Issue - State: open - Opened by idalindegaard 7 months ago

#496 - Pre-set for Quant-it set up on Hamilton

Issue - State: open - Opened by idalindegaard 7 months ago

#495 - Add missing UDF check for Aliquot samples for enzymatic fragmentation TWIST

Issue - State: closed - Opened by Karl-Svard 7 months ago - 1 comment

#494 - Add Raredisease as option in LIMS

Issue - State: closed - Opened by peterpru 7 months ago - 1 comment

#493 - Set prepared_at for RML samples

Issue - State: closed - Opened by islean 8 months ago - 1 comment

#492 - Delete weird old test file

Pull Request - State: closed - Opened by Karl-Svard 8 months ago - 2 comments

#491 - Update concentration input of Saphyr Average concentration and CV calculation script

Pull Request - State: closed - Opened by idalindegaard 8 months ago - 1 comment