Repositories list

• wdl-ci

  Public
  Tools to validate and test WDL-based repositories. To be used as part of CI/CD pipelines

  wdl

  Python

  •

  GNU General Public License v2.0

  •1•5•1•3•Updated Dec 20, 2024Dec 20, 2024

• dnastack-client

  Public
  The command line interface and client library for DNAstack services and GA4GH-compatible service, implemented in Python

  pythonclientworkflow+ 8python3omicsga4ghga4gh-wesdnastackga4gh-data-connectga4gh-service-registry+ 1

  Python

  •

  Apache License 2.0

  •0•0•2•1•Updated Dec 10, 2024Dec 10, 2024

• ga4gh-search-adapter-google-sheets

  Public
  Dataset API wrapper for Google Sheets

  Java

  •

  Apache License 2.0

  •0•1•0•2•Updated Dec 10, 2024Dec 10, 2024

• aws-healthomics-engine-installer

  Public
  HCL

  •

  GNU Lesser General Public License v2.1

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• cromwell-on-gcp-workbench-engine-installer

  Public
  Documentation and tools for creating a Cromwell installation on GCP compatible with DNAstack's Workbench.

  HCL

  •

  GNU Lesser General Public License v2.1

  •0•3•0•0•Updated Nov 26, 2024Nov 26, 2024

• wdl-common

  Public
  Fork of PacBio's wdl-common repo

  WDL

  •

  BSD 3-Clause Clear License

  •6•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• HiFi-human-WGS-WDL

  Public
  WDL

  •

  BSD 3-Clause Clear License

  •31•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• data-connect-trino

  Public
  Cloned from https://github.com/DNAstack/ga4gh-search-adapter-presto

  publisheractivetrino+ 1data-connect

  Java

  •

  Apache License 2.0

  •3•4•2•2•Updated Nov 6, 2024Nov 6, 2024

• cromwell-on-azure-workbench-engine-installer

  Public
  Documentation and tools for creating a CromwellOnAzure installation compatible with DNAstack's Workbench.

  HCL

  •

  GNU Lesser General Public License v2.1

  •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• cromwell-wes-service

  Public
  Java

  •

  GNU Lesser General Public License v2.1

  •1•9•0•0•Updated Aug 22, 2024Aug 22, 2024

• bioinformatics-public-docker-images

  Public
  Dockerfile

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

• bioinformatics-scripts

  Public
  Scripts and resources for the bioinformatics team

  Shell

  •

  GNU General Public License v2.0

  •0•3•0•0•Updated Jan 25, 2024Jan 25, 2024

• fasp-scripts

  Public archive
  Jupyter Notebook

  •

  Apache License 2.0

  •7•0•0•0•Updated Jan 18, 2024Jan 18, 2024

• actuator-e2e-test

  Public
  Library for testing /actuator endpoint

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 3, 2024Jan 3, 2024

• logback-extensions

  Public archive
  Extensions to logback for smoother integration with cloud environments.

  Java

  •

  Apache License 2.0

  •0•0•0•1•Updated Dec 5, 2023Dec 5, 2023

• ismb-2022-ga4gh-tutorial

  Public archive
  ISMB 2022 tutorial on FASP and Starter Kit

  Jupyter Notebook

  •

  Apache License 2.0

  •2•0•0•0•Updated Oct 26, 2023Oct 26, 2023

• gatekeeper

  Public archive
  Gatekeeper

  Java

  •

  Other

  •0•0•0•1•Updated Sep 11, 2023Sep 11, 2023

• wdl-mothur

  Public
  wdl-mothur is a repository featuring a Workflow Description Language (WDL) pipeline for seamless processing of 16S rRNA data using Mothur, enabling reproducible and customizable analysis of microbial communities.

  WDL

  •1•0•1•0•Updated Aug 21, 2023Aug 21, 2023

• sentieon-amazon-omics

  Public
  Sentieon pipelines for Amazon Omics

  WDL

  •

  BSD 2-Clause "Simplified" License

  •4•0•0•0•Updated Aug 2, 2023Aug 2, 2023

• data-explorer

  Public archive
  The simplest, fastest way to get business intelligence and analytics to everyone in your company 😋

  Clojure

  •

  Other

  •5.2k•0•0•0•Updated Jul 31, 2023Jul 31, 2023

• Harmony-RNA-Workflow

  Public
  Workflow for Single-cell RNA Measurements using Seurat

  R

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Jul 26, 2023Jul 26, 2023

• Workbench-Azure-SaaS-Accelerator

  Public
  A reference example with sample code for developers interested publishing transactable, Software as a-Service offers in the Microsoft commercial marketplace.

  C#

  •

  MIT License

  •308•0•0•0•Updated Jun 7, 2023Jun 7, 2023

• ga4gh-discovery-search

  Public archive
  GA4GH Search API specification.

  Apache License 2.0

  •14•1•0•0•Updated May 17, 2023May 17, 2023

• commit-plantuml-action

  Public archive
  This action generate diagrams (png) from PlantUML files (*.puml), and commit to pull-request. Also this can add review comment of diff files.

  Shell

  •

  GNU General Public License v3.0

  •6•0•0•0•Updated May 12, 2023May 12, 2023

• healthcare-federated-access-services

  Public archive
  Go

  •

  Apache License 2.0

  •9•0•0•0•Updated May 9, 2023May 9, 2023

• httpbin

  Public archive
  HTTP Request & Response Service, written in Python + Flask.

  Python

  •

  ISC License

  •1.8k•0•0•0•Updated Apr 12, 2023Apr 12, 2023

• dnastack-wdl-ci

  Public archive
  Github Action for wdl-ci - Test WDL workflows via DNAstack Workbench

  Apache License 2.0

  •0•0•0•0•Updated Mar 2, 2023Mar 2, 2023

• sample-workflows

  Public archive
  Sample bioinformatics workflows

  WDL

  •

  GNU General Public License v2.0

  •0•1•0•0•Updated Feb 8, 2023Feb 8, 2023

• monkeypox-processing-pipeline

  Public archive
  Workflows and containers for analyzing the Monkeypox virus

  WDL

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

• Oxford_Nanopore_ARTIC

  Public archive
  WDL-based analyis of single-ended Oxford Nanopore SARS-CoV-2 reads using the ARTIC pipeline

  WDL

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023