broadinstitute/warp issues and pull requests

#988 - Support for 'prefer not to answer'

Issue - State: open - Opened by mfisher29 over 1 year ago

#987 - Kp moving containers from warp pd 2185

Pull Request - State: open - Opened by kevinpalis over 1 year ago - 5 comments

#986 - Updating feature branch to reduce chances of merge conflicts

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

#985 - Kp moving containers from warp pd 2185

Pull Request - State: closed - Opened by kevinpalis over 1 year ago - 2 comments

#984 - KM Update Optimus Overview doc

Pull Request - State: closed - Opened by kayleemathews over 1 year ago - 2 comments

#983 - Np update star references

Pull Request - State: open - Opened by nikellepetrillo over 1 year ago - 1 comment

#982 - Updating buildIndices inputs

Pull Request - State: open - Opened by nikellepetrillo over 1 year ago - 2 comments

#981 - imputation HG38 support

Issue - State: open - Opened by zhaohongqiangsoliva over 1 year ago

#980 - Updating my feature branch

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

#979 - Biotypes for slide-seq

Issue - State: open - Opened by kzb193 over 1 year ago

#978 - Update multiome.wdl

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 5 comments

#977 - GroupByUMIs memory accessible at top level workflow

Pull Request - State: open - Opened by kachulis over 1 year ago - 5 comments

#976 - Updated slide-seq fastqprocessing to warp-tools docker

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 3 comments

#975 - Add the script used to generate the bge interval list to scripts

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

#974 - Update ATAC wdl to include all tasks

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 10 comments

#973 - Lk pd 2229 update optimus fastqprocessing

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 11 comments

#972 - Make Cross Check Fingerprints Optional in Joint Genotyping Workflow

Pull Request - State: open - Opened by yueyaog over 1 year ago - 2 comments

#971 - [FE-16] Update BroadInternalRNAWithUMIs output metrics fields to round to integers

Pull Request - State: closed - Opened by mmorgantaylor over 1 year ago - 9 comments

#970 - Np update build indices docker

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 3 comments

#969 - Lk modify reference scripts

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 2 comments

#967 - Added metrics task for snapatac2

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 10 comments

#966 - Lk pd 2198 make cb tag atac bam

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 2 comments

#965 - Updated Snapatac2 docker

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 2 comments

#964 - Np create test for multiome

Pull Request - State: open - Opened by nikellepetrillo over 1 year ago - 6 comments
Labels: DO NOT MERGE

#963 - Np multiome wrapper wdl

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 7 comments

#962 - Moved whitelist parameters as input files

Pull Request - State: open - Opened by vsmalladi over 1 year ago - 6 comments

#961 - Add in index file for azure

Pull Request - State: open - Opened by vsmalladi over 1 year ago - 4 comments

#960 - Lk optimus stranded check

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 13 comments

#959 - Np methylome demultiplexing

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 5 comments

#958 - rnaseqc bias edge case patch

Pull Request - State: closed - Opened by kachulis over 1 year ago - 6 comments

#957 - Np add fragment file task

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 8 comments

#956 - Update atac.wdl to handle multiple files

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 2 comments

#955 - [MOCHA-720] eMerge: add `lab_batch` to ImputationInputsTable, ImputationTDR WDL

Pull Request - State: closed - Opened by schaluva over 1 year ago - 5 comments

#954 - Np gene metrics remove cols from optimus and slideseq

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 9 comments

#953 - Lk pd 2182 add barcodes multiome

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 11 comments

#952 - Add RRID to README

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

#951 - KM Update Slide-seq & Optimus Docs

Pull Request - State: closed - Opened by kayleemathews over 1 year ago - 16 comments

#950 - update warp-tools docker

Pull Request - State: closed - Opened by jessicaway over 1 year ago - 5 comments

#949 - Km slide seq doc updates

Pull Request - State: closed - Opened by kayleemathews over 1 year ago - 3 comments

#948 - Lk snapatac2 docker

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

#947 - Create docker with both BWA version 0.7.17 and Samtools.

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 7 comments

#946 - Np remove some columns from optimus cell metrics csv

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 24 comments

#945 - Bump webpack from 5.51.1 to 5.76.1 in /website

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, javascript

#944 - Create atac.wdl

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 15 comments

#943 - Np move bwa mk index into build indices

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 10 comments

#942 - Staging --> master

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 2 comments

#941 - Bump @sideway/formula from 3.0.0 to 3.0.1 in /website

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies, javascript

#940 - Lk methylome

Pull Request - State: open - Opened by ekiernan over 1 year ago - 7 comments

#939 - dev -> staging

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 3 comments

#938 - fix double quotes in changelogs to match master

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

#937 - Disk size calculation for SplitMultiSampleVcf

Pull Request - State: closed - Opened by kachulis over 1 year ago - 8 comments

#936 - Updating docker in UltimaJointGenotyping pipeline

Pull Request - State: closed - Opened by meganshand over 1 year ago - 3 comments

#935 - fix spacing in docktstore yml

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

#934 - Lk pd2126 refence name output

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 6 comments

#933 - Kp improving scitests error reporting pd 2130

Pull Request - State: closed - Opened by kevinpalis over 1 year ago - 3 comments
Labels: eng-only

#932 - dev -> staging

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

#931 - Updating feature branch to reduce chances of conflict

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

#930 - fix input json for scientific optimus test

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 7 comments

#929 - revert --preserve-map-align-order true

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 6 comments
Labels: eng-only

#928 - Updating feature branch with develop

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

#927 - Km optimus doc updates

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 3 comments

#926 - staging to master

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 3 comments

#925 - dev to staging

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

#924 - dynamically size disk in checkOptimusInput

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 2 comments

#923 - dev -> staging

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

#922 - Docker in Ultima Joint Genotyping pipeline is not public

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

#921 - install matplotlib<3.7 to fix scanpy

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 2 comments
Labels: eng-only

#920 - Update Optimus.changelog.md

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

#919 - Fk cloud slideseq

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 39 comments

#918 - Update warp-tools docker version

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 11 comments

#917 - Handle situation with few or zero reads in TCap

Pull Request - State: closed - Opened by kachulis over 1 year ago - 19 comments
Labels: eng-only

#916 - Update human_v3_example.json

Pull Request - State: closed - Opened by aawdeh over 1 year ago - 7 comments

#915 - KM Add UMI metrics task to SlideSeq Overview

Pull Request - State: closed - Opened by kayleemathews over 1 year ago - 3 comments

#914 - Lk pd 2134 optimus chem

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 10 comments

#913 - RNAWithUMIs pipeline fails if there are very few reads

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

#912 - Add input_id to cell metrics and gene metrics outputs of Optimus

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

#911 - Bump http-cache-semantics from 4.1.0 to 4.1.1 in /website

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, javascript

#910 - removed kdeg from doc contacts

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

#909 - Received error when running Exome-Analysis-Pipeline on Terra

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

#908 - adding WARP DOI to getting-started

Pull Request - State: closed - Opened by ekiernan over 1 year ago - 2 comments

#907 - Bump ua-parser-js from 0.7.28 to 0.7.33 in /website

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, javascript

#905 - PD-2100 replace all instances of hca-dcp-mint-test-data/reference with broad-gotc-test-storage

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago - 15 comments

#904 - Kp update emptydrops container pd 2131

Pull Request - State: closed - Opened by kevinpalis over 1 year ago - 12 comments

#899 - KM document slideseq test data

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

#887 - RSEM index for demultiplexed sequence data

Issue - State: closed - Opened by ReshmaRamaiah10 almost 2 years ago - 2 comments

#885 - [DFE-804] updates to MergeMetrics in BroadInternalRNAWithUMIs (reopened)

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

#869 - Improve determinism of RNAWithUMIs pipeline

Pull Request - State: closed - Opened by kachulis almost 2 years ago - 38 comments
Labels: eng-only

#868 - Update ArraysInternalTasks and BroadInternalArrays to accept and ingest `lab_batch`

Pull Request - State: closed - Opened by schaluva almost 2 years ago - 8 comments
Labels: eng-only

#859 - Upgrade WARP to latest release of Picard (2.27.5)

Pull Request - State: open - Opened by nikellepetrillo almost 2 years ago - 3 comments

#846 - Add option for requester pays into joint genotyper (import gvcf)

Pull Request - State: open - Opened by yfarjoun almost 2 years ago - 3 comments

#845 - Km slideseq overview

Pull Request - State: closed - Opened by kayleemathews almost 2 years ago - 18 comments

#842 - rnaseqc undefined behavior for bias metrics in tests.

Issue - State: closed - Opened by kachulis almost 2 years ago - 4 comments

#801 - testing the new sctools docker

Pull Request - State: closed - Opened by khajoue2 about 2 years ago - 11 comments
Labels: DO NOT MERGE

#798 - Test files still inaccessible

Issue - State: closed - Opened by kalong2 about 2 years ago - 2 comments

#785 - Updated a check for an empty file produced in the GetFingerprintingIntervalIndices task in JointGenotypingByChromosomePartOne.wdl.

Pull Request - State: closed - Opened by samuelklee about 2 years ago - 11 comments

GitHub / broadinstitute/warp issues and pull requests