dacs-hpi/covradar issues and pull requests

#251 - Add image tag variable

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#250 - Update .gitlab-ci.yml

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#249 - Update .gitlab-ci.yml

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#248 - Allow insertions in consensus sequence table

Pull Request - State: merged - Opened by jtembrockhaus almost 3 years ago

#247 - Add caching to speed up building images

Pull Request - State: closed - Opened by mirand863 almost 3 years ago

#246 - fix ebi pipeline failing #minor

Pull Request - State: merged - Opened by PaulVII almost 3 years ago

#245 - automatic rki updates #minor

Pull Request - State: merged - Opened by PaulVII almost 3 years ago

#244 - Fix for gene extraction script

Pull Request - State: merged - Opened by jtembrockhaus almost 3 years ago

#243 - Update kubernetes cluster automatically

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#242 - Add bash strict mode

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#241 - Fix version 0 printed on website

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#240 - Deploy to gitlab and staging server with every merge into master

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#239 - Fix date filter bug and formatting

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#238 - Add filter to remove sequences older than 2019

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#237 - Fix/fk creation #patch

Pull Request - State: merged - Opened by PaulVII almost 3 years ago - 1 comment

#236 - Delete script run_mafft_incrementally.py

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#235 - Fix bug in rule bcftools and fix bug in iupac verification and add some tests for rule filter_and_merge

Pull Request - State: merged - Opened by mirand863 almost 3 years ago - 11 comments

#234 - Fix/merged datasets memory #patch

Pull Request - State: merged - Opened by PaulVII almost 3 years ago - 3 comments

#233 - home page updated #patch

Pull Request - State: merged - Opened by Alice_Wittig almost 3 years ago

#232 - Add help page #minor

Pull Request - State: merged - Opened by jtembrockhaus almost 3 years ago
Labels: NAR_inquiry

#231 - fix cov exceeding mysql limits #patch

Pull Request - State: merged - Opened by PaulVII almost 3 years ago

#230 - Resolve "Adapt residue converter to ribosomal slippage"

Pull Request - State: merged - Opened by JakubBartoszewicz almost 3 years ago
Labels: rki

#229 - Restructure additional analysis scripts #minor

Pull Request - State: merged - Opened by jtembrockhaus almost 3 years ago - 1 comment

#228 - voc.tsv with omicron

Pull Request - State: merged - Opened by Alice_Wittig almost 3 years ago

#227 - Analysis scripts documentation + voc.tsv update

Pull Request - State: merged - Opened by jtembrockhaus almost 3 years ago - 1 comment

#226 - Redis caching and new SQL schema #major

Pull Request - State: merged - Opened by PaulVII almost 3 years ago - 4 comments

#225 - Remove insertions from multiple sequence alignment

Pull Request - State: merged - Opened by mirand863 almost 3 years ago

#224 - fix duplicate entry for output of rule split by date #patch

Pull Request - State: merged - Opened by PaulVII about 3 years ago - 2 comments

#223 - Add retries with memory increase

Pull Request - State: merged - Opened by mirand863 about 3 years ago

#222 - Remove isoweek from snakemake rules

Pull Request - State: merged - Opened by mirand863 about 3 years ago

#221 - Remove sleep from snakemake rules

Pull Request - State: merged - Opened by mirand863 about 3 years ago

#220 - Draft:#minor Recent sequences filter

Pull Request - State: opened - Opened by PaulVII about 3 years ago

#219 - #patch: disable voc_of_seqs generation

Pull Request - State: merged - Opened by PaulVII about 3 years ago - 3 comments

#218 - Enforce VARCHAR(500) type for submitting_lab from all sources

Pull Request - State: merged - Opened by mirand863 about 3 years ago

#217 - Update README.md

Pull Request - State: closed - Opened by mirand863 about 3 years ago

#216 - Draft: Covsonar integration

Pull Request - State: closed - Opened by jtembrockhaus about 3 years ago - 1 comment

#215 - fix python version in conda env

Pull Request - State: merged - Opened by Alice_Wittig about 3 years ago

#214 - Add automated gisaid download #minor

Pull Request - State: merged - Opened by PaulVII about 3 years ago - 3 comments

#213 - Right menu fix

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#212 - Fix cronjob to download and run the pipeline for EBI data daily #patch

Pull Request - State: merged - Opened by PaulVII over 3 years ago - 2 comments

#211 - voc.tsv update

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#210 - Voc update

Pull Request - State: closed - Opened by Alice_Wittig over 3 years ago

#209 - Tabular output of base and aa frequencies

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 1 comment
Labels: TODO-Pipeline, priority: mid

#208 - Map circles #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#207 - pip added in environment.yml

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#206 - Data Download Frontend #minor

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 3 comments

#205 - Custom codon input text field width 100%

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago

#204 - Fix Issue 228 - Wrong codons highlighted

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 2 comments

#203 - Ebi download fix #patch

Pull Request - State: merged - Opened by PaulVII over 3 years ago - 15 comments

#202 - Resolve "add tabular output of base frequencies"

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 1 comment
Labels: Nice2have-Website, TODO-Pipeline, priority: mid

#201 - Fix permission problem in some filesystems

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#200 - handle incorrect spacing in location when extracting gisaid #minor

Pull Request - State: merged - Opened by PaulVII over 3 years ago - 3 comments

#199 - voc_of_seqs_error

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 2 comments

#198 - Add gisaid extraction script #minor

Pull Request - State: merged - Opened by PaulVII over 3 years ago - 8 comments

#197 - Bug fix if the rule voc_of_seqs

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago

#196 - Resolve "Error in rule voc_of_seqs_table"

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago
Labels: Bug-Pipeline

#195 - Fix incorrect integer value error

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#194 - Switch all tables to InnDB #minor

Pull Request - State: merged - Opened by PaulVII over 3 years ago

#193 - Renamed VOC to Concerning Amino Acid Mutation in freq plot #minor

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 6 comments

#192 - Mysql schema optimization #minor

Pull Request - State: closed - Opened by PaulVII over 3 years ago - 1 comment

#191 - Bug fixes #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#190 - Germany map #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#189 - Annotation of Frequency Plot + Modals for Plot Descriptions #minor

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago - 2 comments

#188 - Added check before deploying docker images

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#187 - disable debug

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#186 - Fix port for kubernetes cluster

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#185 - Remove page dependency

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#184 - Weekly MOC update

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago

#183 - Small adjustments #minor

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago

#182 - Removed demis_plz

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#181 - Fixed bug that erased lab columns

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#180 - Fix IE Appearance

Pull Request - State: merged - Opened by jtembrockhaus over 3 years ago

#179 - Improved AA plot #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#178 - README.md update

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#177 - voc_update

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#176 - MOC update

Pull Request - State: closed - Opened by jtembrockhaus over 3 years ago
Labels: Research

#175 - Rename primary diagnostic lab pc to sending_lab

Pull Request - State: closed - Opened by mirand863 over 3 years ago

#174 - db information added #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#173 - imprint on homepage and dashboard added #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#172 - Germany map #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#171 - application note link updated #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#170 - WIP: Fix mobile fonts #minor

Pull Request - State: closed - Opened by PaulVII over 3 years ago - 1 comment

#169 - Print output #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#168 - Germany map #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#167 - Plotly scaling workaround #minor

Pull Request - State: merged - Opened by PaulVII over 3 years ago - 1 comment

#166 - Germany map #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#165 - Added threads parameter to raxml

Pull Request - State: closed - Opened by mirand863 over 3 years ago

#164 - Germany map #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#163 - Added parameter "--exportWithInsertions no" to virulign

Pull Request - State: closed - Opened by mirand863 over 3 years ago

#162 - Fixed memory leak in the script voc_of_seqs.py

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#161 - information and link about variants added #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#160 - germany pages deactivated #minor

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

#159 - Optimized disk and memory usage

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#158 - Added conditions to avoid errors when reporting_lab is absent

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#157 - Added script to print CovRadar's version when starting the pipeline

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#156 - Update run_by_cron_get_ebi_data.sh

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#155 - Update pvirulign

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#154 - Update number of threads for virulign

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#153 - Update virulign to parallel version

Pull Request - State: merged - Opened by mirand863 over 3 years ago

#152 - index fix for voc table

Pull Request - State: merged - Opened by Alice_Wittig over 3 years ago

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