jdidion

autoclick

Create Click-based CLIs from python3 type annotations (beta)

OpenBioinformaticsWorkshops

Open courseware for workshops in applied bioinformatics

seqio

A library for high-performance reading and writing of common NGS formats. (pre-alpha)

ngstream

Simple reading/streaming of NGS reads from SRA. (alpha)

audiodrama

My audio drama feeds OPML

docparse

Parse python docstrings (beta)

dxcompiler-compile-action

A GitHub action to compile a WDL workflow using dxCompiler

hon

An opinionated Python project management tool (pre-alpha)

wdlkit

WDL toolkit

.github

Default community-health files for my repos

awesome-nextflow

A curated list of nextflow based pipelines

bioconda-recipes

Conda recipes for the bioconda channel.

blockmute

Use the twitter API to block muted IDs, and vice-versa

bookmark-cleaner

migrate from Chrome bookmarks to Raindrop

bwa-postalt-rs

Reimplementation of BWA alt-aware post-processing in Rust

cwljava

Java SDK for CWL

cwltool

Common Workflow Language reference implementation

dx_app_builder

Apps to build your app/applet/asset from source in a containerized environment.

dxwdl-action-test

fastq-vs-ubam

Compare speed of FASTQ vs uBAM for various applications

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

generative_music

Experiments in generative music. (sandbox)

miniwdl

Workflow Description Language developer tools & local runner

personal-genome-analysis

Guide to personal genome analysis, with code and workflows

pokrok

Use any progress bar package with a simple API (production)

sandbox

Various sandbox projects and one-offs. (unsupported)

sbpack

Command line utility to pack and upload/download CWL to/from SB powered platform

wdl

Workflow Description Language - Specification and Implementations

wdltools-feedstock

A conda-smithy repository for wdltools.

Whole-Foods-Delivery-Slot

Automated script for Whole Foods and Amazon Fresh delivery slot