mskcc/nf-fastq-plus issues and pull requests

#223 - Bump cookiejar from 2.1.2 to 2.1.4 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#222 - Bump json5 from 2.2.0 to 2.2.3 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#221 - Bump flat and mocha in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#220 - Bump jsonwebtoken and express-jwt in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#219 - Bump qs and express in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#218 - Bump express from 4.16.4 to 4.17.3 in /dashboard/api

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#217 - Bump moment from 2.29.1 to 2.29.4 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#216 - Bump node-fetch from 2.6.1 to 2.6.7 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#215 - Bump moment from 2.29.1 to 2.29.2 in /dashboard/api

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#214 - Bump follow-redirects from 1.14.7 to 1.14.8 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#213 - Bump follow-redirects from 1.14.4 to 1.14.7 in /dashboard/frontend

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#212 - Bump follow-redirects from 1.13.3 to 1.14.7 in /dashboard/api

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#211 - Simpler demux part i

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

#210 - Remove I7 & 6NT split sample sheets

Issue - State: closed - Opened by dmcmanam about 3 years ago

#209 - Bump validator from 13.5.2 to 13.7.0 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#208 - WGS Samples do not run Mark Duplicates

Issue - State: closed - Opened by DavidStreid about 3 years ago - 1 comment

#207 - Creating a DRAGEN & bcl2fastq demux for WGS

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

#206 - Sending alerts to DATA_QC_ALERTS for missing FASTQ files

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

#205 - Set completed run files for ruth and pepe sequencers closes #204

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

#204 - Ruth runs may be kicked off before the run is complete

Issue - State: closed - Opened by dmcmanam about 3 years ago - 1 comment
Labels: bug

#203 - Forking PPG Samplesheets to run through DRAGEN

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

#202 - Add script that will re-run just a sample

Issue - State: open - Opened by DavidStreid about 3 years ago

#201 - Helper Scripts for PPG requests

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#200 - Adding Section: Troubleshooting/Common-Issues

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

#199 - Refactor

Issue - State: open - Opened by DavidStreid about 3 years ago

#198 - Adding CRISPRESSO

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#197 - Piping to "sort | uniq" to eliminate duplicate params

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

#196 - Adding method of updating dashboard view

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

#195 - Adding way to update day filter in dashboard

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

#194 - Multiome Demux

Issue - State: open - Opened by DavidStreid about 3 years ago

#193 - Feature/run param config

Pull Request - State: closed - Opened by darrelln32 about 3 years ago

#192 - Feature/run param config

Pull Request - State: closed - Opened by darrelln32 about 3 years ago

#191 - Adding back skipping demux step if output folder already present

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

#190 - FIX: reference names

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#189 - Demultiplex Thread Balancing (--writing-threads 24)

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

#188 - Sometimes Samples stop after MD & Merge

Issue - State: closed - Opened by DavidStreid about 3 years ago - 1 comment

#187 - Alerting instead of failing on Missing FASTQs

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

#186 - TCR SEQ

Issue - State: open - Opened by DavidStreid about 3 years ago

#185 - Prepare 10X for BCL2FASTQ

Issue - State: open - Opened by DavidStreid about 3 years ago

#184 - Convert RNASeq pipeline to use DRAGEN (STAR aligner instead of bwa)

Issue - State: closed - Opened by DavidStreid about 3 years ago

#183 - Updating Makefile - includes docker

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

#182 - Automating DRAGEN alignment for WGS

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

#181 - Refactoring generate_run_params_wkflw

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#180 - Removing RUN_PARAMS_FILE passing

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

#179 - SingleCellCNV should not run Mark Duplicates

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#178 - HemePACT_v4_BAITS: b37 -> b38

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

#177 - Adding UPLOAD_DONE gate

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

#176 - Adding back dgn_ss_split

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#175 - RUN_TAG=RUNNAME_PROJECT_TAG_SAMPLE_TAG_GTAG_RECIPE

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

#174 - demux errorStrategy: 'terminate' => 'ignore'

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

#173 - Update run_param_config.py

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

#172 - Adding FITLER

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

#171 - Adding MiGEC binary

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#170 - Appending RECIPE to RUN_TAG

Pull Request - State: open - Opened by DavidStreid about 3 years ago

#169 - Bump tar from 6.1.5 to 6.1.11 in /dashboard/api

Pull Request - State: open - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#168 - Writing merge commands to file

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

#167 - Adding DRAGEN BAM creation for RNA-Seq

Pull Request - State: open - Opened by DavidStreid about 3 years ago