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DataBiosphere/analysis_pipeline_WDL

Stars
6
Rank 2,539,965 (Top 51 %)
Language WDL
Created over 3 years ago
Updated over 1 year ago

DataBiosphere/analysis_pipeline_WDL

DataBiosphere

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Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

dsub

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

terra-ui

Web user interface for the Terra platform

leonardo

Notebook service

terra-docker

Jupyter Notebook

job-manager

Job Manager API and UI for interacting with asynchronous batch jobs and workflows.

terra-interoperability-model

Common data model proposal for biomedical research intended to facilitate and encourage data sharing and reuse

terra-workspace-manager

jade-data-repo

The Terra Data Repository built by the Jade team.

topmed-workflows

a place for topmed workflows

terra-cli

data-browser

Jupyter Notebook

data-explorer

consent

Broad Institute Data Use Oversight System

data-portal

duos-ui

Broad Institute Data Use Oversight System

consent-ontology

Broad Institute Data Use Oversight System

terra-notebook-utils

Utilities for the Terra notebook environment.

bgzip

Fast streams for block gzip files.

terra-examples

Examples for use in data analysis.

Jupyter Notebook

azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP

getm

Concurrent reads of HTTP URL addressed data

terra-landing-zone-service

hca-ingest

terra-app

FHIR

Broad FHIR is a FHIR Server that powers applications for Genomics research.

sync-github-labels

Synchronize Github issue and PR labels between two repositories

terra-cloud-resource-lib

terra-resource-buffer

Terra Resource Buffering Service

terra-external-credentials-manager

terra-axon-examples

Example notebooks and documentation for working with the Terra Axon UI.

terra-billing-profile-manager

terra-workspace-data-service

terra-java-project-template

herzog

Version control, test, and CI/CD your Python Jupyter notebooks.

jade-data-repo-ui

UI for the Jade Data Repo

data-explorer-indexers

bard

Metrics collection service

consent-data-use

encode-ingest

Batch ETL pipeline to mirror ENCODE data into the Jade Data Repository.

welder

clinvar-ingest

Batch ETL pipeline to mirror ClinVar releases into the Jade Data Repository.

xsamtools

Lightly modified versions of htslib and bcftools to merge VCF streams.

terra-policy-service

data-store

AWS and GCP data storage system for genomic data.

calhoun

Notebook preview service

Jupyter Notebook

terra-azure-relay-listeners

consent-ui

Broad Institute Data Use Oversight System

commons-sample-data

A repo to track various TOPMed and other datasets

github-actions

Data Biosphere GitHub Actions

wdl-conformance-tests

topmed-workflow-variant-calling

saturn-ui-prod-deploy

Terra UI automated prod deploy service

cbas

biocore-data-model

BioCore Data Model

Jupyter Notebook

tanagra

Repo for the Tanagra service being developed by the All of Us DRC

terra-aws-resource-discovery

firecloud-app

terra-drs-hub

terra-axon-ui

Repository for the Terra "Axon" UI

kernel-service-poc

featured-notebooks

dos-azul-lambda

Provides access to DSS azul-index in the Data Object Service schemas

Jupyter Notebook

rex

Survey response service

terra-gcs-bq-streaming-functions

stairway

Stairway saga transaction processor library

terra-resource-janitor

Janitor service to cleanup resources created by Cloud Resource Library (CRL)

ssds

Simple data storage system for AWS and GCP

example-authz-registry

example of maintaining authorization list via github + travis + s3

transporter

Bulk file-transfer system for data ingest

newt-transformer

Amphibious new data transformer to prepare various sources for CGP DSS Data Loader

lyle

Test user allocation service

bard-client

JavaScript library for shared client-side analytics across DSP

bond

Account linking service

env-base

Base framework environment k8s resources

hca-metadata-api

A library for processing HCA metadata programmatically

data-store-auth

data-store authentication infra management

java-pfb

terra-azure-arm-templates

saturn-terraform

Terraform definitions for all Saturn-managed repos and GCS projects

metadata-serialization

Serializing metadata for use and reuse ✒️📋🗃️💻

hamm

Cloud Cost Management Service

wdl-parsers

A package that provides the generated ANTLR4 WDL parsers for Python.

saturn-documentation

bdcat-integration-tests

This supports integration testing between components for the biodata catalyst grant.

terra-folder-manager

hca-import-validation

A utility to validate a staging area before it is imported.

terra-test-runner

terra-data-catalog

data-platforms

Components of the Commons Alliance

Jupyter Notebook

cbas-ui

findable-ui