Ecosyste.ms: Issues

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GitHub / molgenis/ngs_automated issues and pull requests

#330 - etc config added concordence check notifications

Pull Request - State: closed - Opened by scimerman 3 months ago

#329 - included notification for ConcordanceCheck

Pull Request - State: closed - Opened by Gerbenvandervries 3 months ago

#326 - fixing rawDataCopiedToPrm issue for RNA pipeline

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

#325 - added copying of samplesheet to results folder for nanopore

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

#323 - missing var

Pull Request - State: closed - Opened by Gerbenvandervries 5 months ago

#322 - small fix for stats.tsv file

Pull Request - State: closed - Opened by RoanKanninga 5 months ago

#321 - added --constraint

Pull Request - State: closed - Opened by RoanKanninga 6 months ago

#320 - added NGS_RNA functionality in moveAndCheckSamplesheets

Pull Request - State: closed - Opened by RoanKanninga 6 months ago

#319 - added checksum to rsync command

Pull Request - State: closed - Opened by RoanKanninga 7 months ago

#318 - shorter interval cleaning up project data

Pull Request - State: closed - Opened by RoanKanninga 7 months ago

#317 - calculating md5s on nanopore machine

Pull Request - State: closed - Opened by RoanKanninga 7 months ago

#316 - Nanopore pipeline: update VIP 7.7.1 to 7.9.0

Pull Request - State: closed - Opened by dennishendriksen 7 months ago

#315 - added check to copyRawNanoporeDataToTmp

Pull Request - State: closed - Opened by RoanKanninga 8 months ago

#314 - first version NP to prm

Pull Request - State: closed - Opened by Gerbenvandervries 8 months ago

#313 - improved first version startNanoporePipeline

Pull Request - State: closed - Opened by RoanKanninga 8 months ago

#312 - introduce startNanoporePipeline.sh 'walking skeleton'

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

#309 - createInhouseSamplesheetFromGS python2 dependency removed

Pull Request - State: closed - Opened by kdelange 9 months ago

#306 - make pullAndProcessGSRawData.sh also fit for RNA projects

Pull Request - State: closed - Opened by kdelange 10 months ago

#305 - fixing moveSequencing data

Pull Request - State: closed - Opened by RoanKanninga 10 months ago

#304 - distinguish between (s)WGS and WES data

Pull Request - State: closed - Opened by RoanKanninga 11 months ago

#302 - added sWGS workflow option

Pull Request - State: closed - Opened by RoanKanninga 11 months ago

#301 - nextflow pipeline

Pull Request - State: closed - Opened by RoanKanninga about 1 year ago

#300 - fixing 2 bugs

Pull Request - State: closed - Opened by RoanKanninga about 1 year ago

#299 - small update trendanalysis, lower threshold from 80 to 50 ng/ul

Pull Request - State: closed - Opened by kdelange about 1 year ago

#298 - fix when there is no samplesheet

Pull Request - State: closed - Opened by RoanKanninga about 1 year ago

#297 - updated config files, so logging for demultiplexing will work

Pull Request - State: closed - Opened by kdelange about 1 year ago

#296 - Replaced cf-transfer on Merlin with new cf-transfer on Bateleur.

Pull Request - State: closed - Opened by pneerincx about 1 year ago

#294 - creating correct file when rawdata is copied to prm

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

#293 - added cleaning up of NGS_Demultiplexing data

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

#291 - fixing cleanupDataOnTmp

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

#290 - update umcg-gd.cfg for trendanalysis

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

#289 - updated trendanalysis

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

#286 - fixing some last errors/bugs in the DRAGEN workflow

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

#285 - Added etc/umcg-pr.cfg.

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

#284 - Bugfix for copyBclDataToPrm.sh

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

#283 - removed 2 unused notifications out of the array

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

#282 - fixing mac2unix/dos2unix issues for samplesheets other than GD

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

#281 - Fix/labgnkbh

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

#280 - Updated logs for notifications.

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

#278 - Deleted old cronjob templates.

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

#277 - Improved handling of notifications.

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

#276 - copyProjectDataToPrm will copy project data to prm when we did not start with rawdata

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

#275 - changing messageBody when > 10 lines

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

#273 - added logging step to copyTrendAnalysisDataToPrm.sh

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

#272 - changed way of logging for the trendanalysis

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

#271 - added variable trandanalysis

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

#270 - fix moving Samplesheet

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

#269 - added extra rm files from trendanalysis/tmp folder

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

#268 - distributing samplesheet to all dat folders

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

#267 - added new pipeline steps to genomescan group

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

#266 - Feature/teams

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

#264 - small bug fix copyTrendanalysisToPrm

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

#263 - Improved indentationcheck

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

#262 - Synced syntax with common code in other repos.

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

#261 - renaming logfile

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

#260 - important bugfix for dragen pipeline

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

#258 - fix issue with copy samplesheet from the wrong location

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

#257 - updated trendanalysis

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

#256 - updates trendAnalyse.sh and copyQCDataToTmp.sh

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

#255 - new script to copy QC data to tmp for trendanalysis

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

#254 - added a genomescan check in the movesamplesheets

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

#252 - multiple new stuff (see comment)

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

#251 - added 'rm /trendanalysis/tmp/*' at the beginning of the script

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

#250 - updated trendanalysis

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

#249 - fix and renaming moveSamplesheets to moveAndCheckSamplesheets + updated config files

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

#248 - minor changes

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

#247 - see comment for what is in PR

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

#246 - updated json files for nicer trendAnalysis html output

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

#244 - added fastqc multiQC metrics to umcg-gd-cfg

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

#243 - removed Jenkinsfile

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

#242 - added functionality to monitor GC% in trendanalysis

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

#241 - added new sequencer to plot

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

#240 - added bucket system and get NGS_Automated working on betabarrel

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

#239 - removed echo statement

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

#238 - SCR_LFS ==> variable instead of hardcoded

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

#237 - small update for wingedhelix

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

#236 - added new script (copyRawDataToTmp) + additional cfg changes to make that script work

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

#235 - updated configs

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

#234 - Improved bin/copyProjectDataToPrm.sh

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

#233 - fixe typo in copyProjectDataToPRM

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

#231 - updated with gendercheck for array pipelines

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