adamstruck

cwl2wdl

Convert CWL to WDL

cwltool

Common Workflow Language reference implementation

funnel

Funnel runs your tasks on Google Cloud, HTCondor, locally, and more.

task-execution-schemas

adamstruck.github.io

Personal Website

Amazon-S3-FileSystem-NIO2

An S3 File System Provider for Java 7

badger

Fast key-value DB in Go.

batchit

simple jobs submission via command-line for AWS batch

bunny

Reproducible Analyses for Bioinformatics - Java

centaur

Cromwell integration testing environment

CGP-Somatic-Docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore

cgpbox

Core calling tools in a convenient docker image

cromwell

Workflow Execution Engine using WDL

cube

📊 Cube — The Semantic Layer for Building Data Applications

cytoscape.js-popper

A wrapper for Popper.js that lets you position divs relative to Cytoscape elements

docker-shiny-server

Docker container for Shiny Server

ebsmount

Mount and unmount EBS volumes on an EC2 instance

fastq2bam

Convert lane level fastq files to unaligned BAM files with PCAWG style header

genetorrent-tool

grip

Graph Database for integrative Analysis

grip-viewer

grpc-gateway

gRPC to JSON proxy generator following the gRPC HTTP spec

homebrew

:beer: The missing package manager for OS X.

jslt

JSON query and transformation language

ophion

Language for making graph queries from data

querybook

Querybook is a Big Data Querying UI, combining collocated table metadata and a simple notebook interface.

Seqware-BWA-Workflow

This is the BWA workflow used in the PanCancer project used to allign all the BAM files.

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

vcf2maf-tools

Suite of tools from https://github.com/mskcc/vcf2maf/

wdl_workflow_app

Webservice for managing and running WDL workflows