Welcome to gwf

gwf is a flexible, pragmatic workflow tool for building and running large, scientific workflows. It runs on Python 3.8+ and is developed at GenomeDK, Aarhus University.

Examples

To get a feeling for what a gwf workflow looks like, have a look at a few examples.

Getting started

To quickly get started writing workflows in gwf you can read the Tutorial.

Features

  • Easy to adopt, there’s no special syntax to learn if you already know Python

  • Automatically resolves dependencies between targets based on filenames

  • Only submits targets when their output files are not up to date

  • Supports multiple backends like Slurm, SGE and a local backend for testing

  • Fire-and-forget, does not require you to use screen or tmux to keep your workflow running

  • Commands for cleaning temporary data from your workflow

  • Friendly to your system administrator!

Installation

We’ll assume that you have the Anaconda distribution installed and that you are familiar with how to install and manage packages and environments through the conda package manager.

To install gwf via Conda:

conda config --add channels gwforg
conda install gwf

We recommend that you install gwf in a project-specific environment:

conda config --add channels gwforg
conda create -n myproject gwf dep1 dep2 ...
conda activate myproject

You can find the code for gwf here. You are encouraged to report any issues through the issue tracker, which is also a good place to ask questions.

User’s Guide

Extending

Release history