broadinstitute/warp-tools issues and pull requests

#100 - PD-2474: Remove reads from MT genes in Tagsort metrics

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

#100 - PD-2474: Remove reads from MT genes in Tagsort metrics

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

#99 - Lk pd2453 bb to cb

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

#98 - Lk pd 2448 add pairedtag upstools

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

#97 - PD-2435 Build docker off branch from forked distributed bwa-mem2

Pull Request - State: closed - Opened by aawdeh about 1 year ago
Labels: do not merge

#96 - PD-2435 Build docker with Intel distributed BWA-MEM2

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

#96 - PD-2435 Build docker with Intel distributed BWA-MEM2

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

#95 - Create upstools.yml

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

#95 - Create upstools.yml

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

#94 - Update docker_versions.tsv to include new docker image

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

#93 - updated docker with timestamp for latest tagsort changes

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

#92 - PD2396 Added "number of output files" as a parameter to fastqprocess

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

#91 - Kp containerize patching script pd 2400

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

#90 - Fixes for refseq data processing

Pull Request - State: closed - Opened by khajoue2 over 1 year ago

#90 - Fixes for refseq data processing

Pull Request - State: closed - Opened by khajoue2 over 1 year ago

#89 - Applied intronic exonic gene counts to unique mappers

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

#89 - Applied intronic exonic gene counts to unique mappers

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

#88 - Automating Docker Builds and Pushes to Azure Container Registry

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

#88 - Automating Docker Builds and Pushes to Azure Container Registry

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

#87 - Create dynamic-barcode-orientation.py

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

#87 - Create dynamic-barcode-orientation.py

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

#86 - Created docker with Debian base image for Samtools and BWA

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

#86 - Created docker with Debian base image for Samtools and BWA

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

#85 - Changed to Debian base image

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

#85 - Changed to Debian base image

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

#84 - Update mitochondrial_gene_selector.cpp

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

#84 - Update mitochondrial_gene_selector.cpp

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

#83 - Lk example print sf

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

#82 - updated STAR docker to 2.7.11a

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

#82 - updated STAR docker to 2.7.11a

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

#81 - Lk example print sf

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

#81 - Lk example print sf

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

#80 - Update Dockerfile for bwa-mem2-lisa

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

#80 - Update Dockerfile for bwa-mem2-lisa

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

#79 - just try to patch trivvy, dont update vbid

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

#78 - update warp tools docker to build latest scripts

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

#77 - update VBID version

Pull Request - State: closed - Opened by nikellepetrillo over 1 year ago
Labels: do not merge

#76 - Update Dockerfile in Samtools with new entrypoint

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

#76 - Update Dockerfile in Samtools with new entrypoint

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

#75 - Created Dockerfile for bwa-mem2-lisa

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

#75 - Created Dockerfile for bwa-mem2-lisa

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

#74 - Adding a different path for tini. It looks like Ubuntu installs it differently

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

#74 - Adding a different path for tini. It looks like Ubuntu installs it differently

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

#73 - Decode fragChrom column in fragment matrix

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

#73 - Decode fragChrom column in fragment matrix

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

#72 - update snaptools_bwa docker

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

#71 - Adding automation for build indices.

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

#71 - Adding automation for build indices.

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

#70 - update eagle and umi tools docker / trivvy vulnerability

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

#70 - update eagle and umi tools docker / trivvy vulnerability

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

#69 - Added comments and upversioned h5py

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

#69 - Added comments and upversioned h5py

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

#68 - PD-2231: Add tests to modified Warp-tools code

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

#68 - PD-2231: Add tests to modified Warp-tools code

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

#67 - fix subread Dockerfile

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

#67 - fix subread Dockerfile

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

#66 - Adding pysam to warp-tools

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

#66 - Adding pysam to warp-tools

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

#65 - Update Readme

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

#64 - Create CI for m3c Dockerfile

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

#63 - Move snM3C Dockerfiles from warp to warp-tools

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

#62 - Move snM3C dockerfiles to warp-tools

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

#61 - Lk star 2.7.10b update

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

#61 - Lk star 2.7.10b update

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

#60 - qa -- do not merge

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

#59 - Update SnapATAC2 version to 2.3.1

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

#59 - Update SnapATAC2 version to 2.3.1

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

#58 - Update docker_versions.tsv

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

#58 - Update docker_versions.tsv

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

#57 - Add tab to read name for add CB task

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

#57 - Add tab to read name for add CB task

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

#56 - Update TagSort to work with RefSeq gtf

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

#56 - Update TagSort to work with RefSeq gtf

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

#55 - Lk picard drop seq docker

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

#54 - Adding automation for more containers

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

#54 - Adding automation for more containers

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

#53 - Update CB/CR tag position in the read header

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

#53 - Update CB/CR tag position in the read header

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

#52 - add cutadapt docker

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

#51 - Continuing work on automating build for all 3rd-party containers for WARP

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

#50 - This creates automation (CI) for all the 3rd party tools containers for WARP

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

#49 - Lk pd 2190 make h5ad

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

#49 - Lk pd 2190 make h5ad

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

#48 - Install gsutil in docker

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

#47 - Reorganizing directories for ease of use and automation.

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

#47 - Reorganizing directories for ease of use and automation.

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

#46 - Build docker with bwa-mem2 and samtools

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

#46 - Build docker with bwa-mem2 and samtools

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

#45 - Kp moving containers from warp pd 2185

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

#44 - Updating my feature branch

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

#43 - test branch for QA

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

#43 - test branch for QA

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

#42 - Update samplefastq

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

#42 - Update samplefastq

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

#41 - Kp adding gtest pd 2211

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

#41 - Kp adding gtest pd 2211

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

#40 - Update docker_versions.tsv

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

#40 - Update docker_versions.tsv

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

#39 - Kp intro to pytest pd 2212

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

#39 - Kp intro to pytest pd 2212

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

GitHub / broadinstitute/warp-tools issues and pull requests