Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Clinical-Genomics/cg_lims issues and pull requests

#397 - Add plugin for sequencing quality control

Issue - State: closed - Opened by seallard over 1 year ago

#396 - Transfer and update check_indexes_before_aliquot.py

Issue - State: open - Opened by Karl-Svard over 1 year ago

#395 - Add Hamilton Normalization and pooling to step CG002 - Normalization of microbial samples for sequencing

Issue - State: closed - Opened by idalindegaard over 1 year ago - 2 comments
Labels: Effort: Small, enhancement

#394 - add_new_lims_verification_issue_template

Pull Request - State: closed - Opened by idalindegaard over 1 year ago - 4 comments

#393 - Add DV200 value to the Tapestation step in RNA RC

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

#392 - Bug in index2 barcode mismatch calculation for NovaSeqX sample sheet

Issue - State: closed - Opened by diitaz93 over 1 year ago - 6 comments
Labels: bug, NovaSeq X

#391 - Verification NovaSeq 6000 v1 workflow

Issue - State: closed - Opened by amandaraud over 1 year ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Verification issue, NovaSeq X

#390 - Initial testing of NovaSeq X v1 workflow

Issue - State: closed - Opened by idalindegaard over 1 year ago - 9 comments
Labels: Effort: Medium, Gain: Large, NovaSeq X

#389 - Initial testing Queue Samples for Sequencing v1 workflow

Issue - State: closed - Opened by amandaraud over 1 year ago - 1 comment
Labels: Effort: Medium, NovaSeq X

#388 - Update the Development Projects Workflow in LIMS

Issue - State: closed - Opened by idalindegaard over 1 year ago - 1 comment
Labels: Effort: Medium, Gain: Medium

#387 - Add TGA sample fetching script

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

#386 - Add new option to move-samples EPP

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

#385 - Add EPP to attach and parse sequencing xml files

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

#384 - Add BarcodeMismatches support to sample sheet generation

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

#383 - WGS qPCR Place Samples in Columns

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

#382 - Update SQL database passwords for clinical_EPPs config

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

#381 - Add new EPP for performing normalization of pools before sequencing

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

#380 - Add new EPPs for calculating NovaSeq X sequencing volumes

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

#379 - New script needed to calculate normalization volumes for covid pools (WF: SARS-CoV-2 v4)

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 1 comment
Labels: Urgency: Medium, Gain: Large

#377 - Verification of new workflow version: TWIST v8

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Large, Urgency: Large, Gain: Large, Verification issue

#376 - Verification of new workflow version: SARS-CoV-2 v4

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 4 comments
Labels: Effort: Large, Urgency: Large, Gain: Large, Verification issue

#375 - Verification of new workflow version: RNA v4

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#374 - Verification of new workflow version: RML v8

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#373 - Verification of new workflow version: Development Projects v4

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#372 - Verification of new workflow version: Microbial WGS v7

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#371 - Verification of new workflow version: NIPT v2

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#370 - Verification of new workflow version: WGS PCR free v6

Issue - State: closed - Opened by idalindegaard almost 2 years ago - 3 comments
Labels: Effort: Medium, Urgency: Large, Gain: Large, Verification issue

#369 - Add normalisation for metagenome WGS samples

Issue - State: closed - Opened by amandaraud almost 2 years ago - 3 comments

#368 - Add new Sample Sheet v2 functionalities

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

#367 - NovaSeq X integration

Issue - State: closed - Opened by Karl-Svard almost 2 years ago
Labels: Effort: Large, Urgency: Large, Gain: Large

#366 - Calculate input amount based on actual concentration, no speedvaccing

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

#365 - Skip Reception Control QC steps

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

#364 - New data from lims

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

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

Issue - State: closed - Opened by amandaraud almost 2 years ago - 2 comments
Labels: Effort: Small, good first issue

#362 - Add RC method document in TGA Aliquotation

Issue - State: closed - Opened by amandaraud almost 2 years ago - 2 comments
Labels: Effort: Small, good first issue

#361 - Add H2O lot number in a lims step

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

#359 - Add new template for manual backup verifications

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

#358 - Edit Library Preparation Method choices in WGS aliquotation

Issue - State: closed - Opened by amandaraud almost 2 years ago - 1 comment
Labels: Effort: Small, good first issue, Urgency: Small

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

Issue - State: closed - Opened by idalindegaard almost 2 years 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 almost 2 years ago - 1 comment
Labels: bug

#354 - TWIST QC RC Quantit new info column

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

#353 - cfDNA update for make_kapa_csv.py

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

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

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

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

Issue - State: closed - Opened by VasKyriak almost 2 years ago - 5 comments

#350 - Add nuclease free H2O to step in TGA

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

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

Issue - State: open - Opened by MarcelaGa almost 2 years 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 almost 2 years ago - 4 comments
Labels: Urgency: Small

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

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

#344 - Update of 96 well placement map EPP

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

#343 - Update Kapa Debug script with new method document

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

#341 - Bait set version missing in Development workflow

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

#339 - Change default to quantit

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

#334 - Small adjustments for reception control in lims

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

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

Issue - State: closed - Opened by VasKyriak over 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 over 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 over 2 years ago - 1 comment

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

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

#329 - Update CODEOWNERS

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

#328 - More detailed error description

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

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

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

#326 - Add measurement level

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

#325 - Add support for tagmentation in RB buffer calc

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

#324 - make the barcodes shorter and sort them

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

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

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

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

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

#321 - New Return Samples WF

Issue - State: closed - Opened by RasmusBurge-CG over 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 over 2 years ago

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

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

#316 - Add Barcodes at Clinical Genomics to RC WGS

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

#315 - Add Atlas link for manual KAPA in lims

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

#314 - Adds script to assigned barcodes

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

#313 - Adds script that generates barcodes

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

#312 - Add method instructions to Atlas Illumina_COVIDseq_on_Hamilton

Issue - State: closed - Opened by MarcelaGa over 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

#299 - Add Placement Map and fix minor things in step "Normalization of microbial samples v2" micro WGS

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

#298 - Barcode generator EPP

Issue - State: closed - Opened by RasmusBurge-CG over 2 years ago - 5 comments
Labels: Effort: Medium, Urgency: Medium, Gain: Medium