dacs-hpi/covradar issues and pull requests

#351 - Minor New api fix

Pull Request - State: opened - Opened by BastianHentschel about 1 year ago

#350 - Draft: Mamba replacement

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

#349 - Mutation speedup

Pull Request - State: merged - Opened by BastianHentschel over 1 year ago

#348 - Mutation plot speedup

Pull Request - State: merged - Opened by BastianHentschel over 1 year ago - 3 comments

#347 - sped up mutation_time_plot

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

#346 - Update .gitlab-ci.yml file

Pull Request - State: merged - Opened by Alice_Wittig almost 2 years ago

#345 - bug fix ini map

Pull Request - State: merged - Opened by Alice_Wittig almost 2 years ago

#344 - restrict flask server to main process

Pull Request - State: merged - Opened by Alice_Wittig almost 2 years ago

#343 - update publication link on covradars homepage

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

#342 - Draft: add docstring in update_map

Pull Request - State: closed - Opened by derBlaumond over 2 years ago - 21 comments

#341 - pyarrow installed via pip not conda

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#340 - Draft: last stable version

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

#339 - Ebi download fix if 500 server response

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#338 - Draft: Ebi download fix if 500 server response

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#337 - create database included in mysqldump

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#336 - Resolve "Remove SQL dumps of the app tests" #minor

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#335 - Update README.md

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#334 - Adjust analysis scripts with new paths in Snakefile

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago - 2 comments

#333 - Fix for empty sequence_voc table in DB

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#332 - Update readme

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#331 - Modus argument added in create_config.py #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#330 - Gisaid logos deactivated

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#329 - min date fix in global map for date previous 25/1/21

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#328 - readme updated

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#327 - Backend Dockerfile

Pull Request - State: merged - Opened by hoelzer over 2 years ago - 3 comments
Labels: WIP

#326 - Adapted PDF track of the Pipeline

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#325 - merge Optimize plot loading into parallelize_mutation_time_plots

Pull Request - State: merged - Opened by fischer-hub over 2 years ago

#324 - Revert "Merge branch 'master' into 'parallelize_mutation_time_plots'"

Pull Request - State: closed - Opened by fischer-hub over 2 years ago

#323 - Master into parallelize_mutation_time_plots

Pull Request - State: merged - Opened by fischer-hub over 2 years ago

#322 - removed pickle

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#321 - data.py updated

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#320 - bugfix types in data.py

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

#319 - bugfix for pickle update in production

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#318 - workflow for ebi data download

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#317 - Filter merge no seqs

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#316 - Bugfix

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#315 - General db names

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#314 - deactivate staging

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#313 - sequence number limit option #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#312 - Snpsql

Pull Request - State: merged - Opened by fischer-hub over 2 years ago

#311 - Snp sql mut dist

Pull Request - State: merged - Opened by fischer-hub over 2 years ago

#310 - Snp sql mut dist

Pull Request - State: closed - Opened by fischer-hub over 2 years ago

#309 - Global statistic table patch

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#308 - Pickle volume #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#307 - raxml-ng output removed from basic statistics

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#306 - Rules cleanup #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#305 - Draft:Parallelize mutation time plots

Pull Request - State: closed - Opened by fischer-hub over 2 years ago

#304 - Improve speed inserting data in both consensus and base_count tables

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#303 - Fix memory leak on consensus script

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#302 - Fix postal codes not being inserted in metadata table

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#301 - Sign URLs for 24h instead of 1h

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#300 - Add workflow to upload databases to kubernetes cluster

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#299 - allow local infile

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#298 - Optimize plot loading

Pull Request - State: closed - Opened by fischer-hub over 2 years ago

#297 - optimize mutation dist plot and consensus map loading time

Pull Request - State: closed - Opened by fischer-hub over 2 years ago

#296 - Fix for map (when only a single mutation is selected)

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#295 - Add conda-forge

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#294 - Remove Germany from GISAID download and add DESH

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#293 - Fix DB info for databases

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#292 - improved VCF performance

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#291 - Update backend/configs/download_gisaid.yml

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#290 - Update paths

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#289 - ray and batches for voc_of_seqs

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#288 - ray set to local mode

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#287 - Vcf compressed

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#286 - Fix region bug

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#285 - Add snakemake pipeline to download gisaid data automatically

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#284 - updated voc.tsv + script for generation #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#283 - Frontend adjustments NAR #minor

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago - 1 comment

#282 - Reactivate Gisaid Infos (Header, Footer, Acknowledgement)

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#281 - ray instead joblib in variant calling

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#280 - Fix unrecognized arguments error

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#279 - batches for variant calling script

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#278 - Landing page

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#277 - Fix empty consensus table

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#276 - Enhanced ebi download

Pull Request - State: merged - Opened by PaulVII over 2 years ago

#275 - World map #major

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#274 - Parallelization of the VCF rule

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#273 - Update encoding for location coordinates

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#272 - Add sql to create location coordinates table

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#271 - Remove pos being printed

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#270 - Fix git clone command

Pull Request - State: closed - Opened by mirand863 over 2 years ago

#269 - Merge EBI and DESH #minor

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#268 - Fix bug if country is NaN

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#267 - Raxml

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#266 - Draft: Advanced Filter Options + Cosmetics

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

#265 - commets on deletions and frame shifts added to residue converter README.md

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#264 - Fix memory leak on script split_by_region.py

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#263 - Add lineage

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#262 - Draft pd as datasource instead of sql

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

#261 - multithreading of voc_of_seqs rule #minor

Pull Request - State: merged - Opened by Alice_Wittig over 2 years ago

#260 - Download option for germany map

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago - 5 comments

#259 - Download option for frequency plot

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago - 2 comments

#258 - Gisaid logos

Pull Request - State: merged - Opened by PaulVII over 2 years ago - 1 comment

#257 - addition of common_omicron label

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago
Labels: NAR_manuscript

#256 - Addition of common_omicron label

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

#255 - Draft:Init cache

Pull Request - State: opened - Opened by PaulVII over 2 years ago

#254 - Add flag to skip german sequences

Pull Request - State: merged - Opened by mirand863 over 2 years ago

#253 - Updated consensus info modal

Pull Request - State: merged - Opened by jtembrockhaus over 2 years ago

#252 - Possibility to subsample input data in pipeline #minor

Pull Request - State: closed - Opened by jtembrockhaus over 2 years ago - 11 comments

GitLab.com / dacs-hpi/covradar issues and pull requests