Broad Institute

Repositories

• wfl

  WorkFlow Launcher (née Zero)
  Clojure BSD-3-Clause 0 8 0 5 Updated Jun 24, 2021

• cromwell

  Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

  docker application workflow cloud bioinformatics scala executor
  Scala 241 701 696 31 Updated Jun 24, 2021

• ddp-study-server

  Pepper Study Server
  Java BSD-3-Clause 0 4 0 18 Updated Jun 24, 2021

• ddp-angular

  Angular code for participant-facing pepper studies
  TypeScript 1 1 0 13 Updated Jun 24, 2021

• warp

  WDL Analysis Research Pipelines
  wdl BSD-3-Clause 20 50 5 10 Updated Jun 24, 2021

• single_cell_portal_core

  Rails/Docker application for the Broad Institute's single cell RNA-seq data portal

  rna-seq-analysis single-cell-genomics human-cell-atlas
  Ruby BSD-3-Clause 19 40 0 1 Updated Jun 24, 2021

• ml4h
  1 package Python 3 14 30 (1 issue needs help) 14 Updated Jun 24, 2021

• rawls

  Rawls service for DSDE
  Scala 2 13 0 14 Updated Jun 24, 2021

• firecloud-orchestration
  Scala BSD-3-Clause 4 22 0 3 Updated Jun 24, 2021

• covid19-testing

  COVID-19 Diagnostic Processing Dashboard
  HTML MIT 2 18 2 0 Updated Jun 24, 2021

• palantir-workflows

  Utility workflows for the DSP palantir team
  wdl BSD-3-Clause 1 7 3 3 Updated Jun 24, 2021

• Drop-seq

  Java tools for analyzing Drop-seq data
  Java MIT 25 81 14 1 Updated Jun 24, 2021

• push-to-cloud-service

  This is the repo for the WorkFlow Launcher's PTC server
  Clojure BSD-3-Clause 0 3 0 1 Updated Jun 24, 2021

• carrot
  Rust 0 0 71 3 Updated Jun 24, 2021

• import-service

  Terra Import Service
  Python BSD-3-Clause 0 1 0 2 Updated Jun 24, 2021

• getzlab-SignatureAnalyzer

  Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
  Python MIT 8 33 7 0 Updated Jun 24, 2021

• genus
  Jupyter Notebook MIT 0 1 3 0 Updated Jun 24, 2021

• gatk

  Official code repository for GATK versions 4 and up

  science bioinformatics spark genomics genome ngs sequencing
  Java 419 1,063 995 (8 issues need help) 93 Updated Jun 24, 2021

• gatk-sv
  wdl BSD-3-Clause 18 53 40 6 Updated Jun 24, 2021

• long-read-pipelines

  Long read production pipelines

  pipelines wdl variant-calling de-novo-assembly long-reads
  Jupyter Notebook BSD-3-Clause 4 45 35 (5 issues need help) 4 Updated Jun 24, 2021

• seqr

  web-based analysis tool for rare disease genomics
  Python AGPL-3.0 56 111 55 2 Updated Jun 24, 2021

• for_ucsc
  0 0 0 0 Updated Jun 24, 2021

• viral-pipelines

  viral-ngs: complete pipelines
  wdl 13 23 12 4 Updated Jun 24, 2021

• ddp-study-manager-ui

  Pepper Study Manager UI
  TypeScript BSD-3-Clause 0 1 0 5 Updated Jun 24, 2021

• monster-deploy

  Infrastructure-as-code for Monster team's "core" environments
  HCL BSD-3-Clause 0 2 0 0 Updated Jun 24, 2021

• ddp-study-manager

  Pepper Study Manager
  3 packages Java BSD-3-Clause 1 2 0 12 Updated Jun 24, 2021

• sam

  workbench identity and access management
  Scala BSD-3-Clause 6 19 2 0 Updated Jun 24, 2021

• neural-profiling
  Jupyter Notebook 0 0 1 0 Updated Jun 24, 2021

• terra-helm

  A helm repo for Terra from Broad Data Science Platforms Group
  Smarty BSD-3-Clause 1 7 0 3 Updated Jun 24, 2021

• datarepo-helm-definitions

  Helm deployment specific values and definitions for Dev, Integration and Prod
  Shell 0 2 0 8 Updated Jun 24, 2021