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https://github.com/chanzuckerberg/miniwdl

Workflow Description Language developer tools & local runner
https://github.com/chanzuckerberg/miniwdl

wdl workflow-description-language

Last synced: 7 days ago
JSON representation

Workflow Description Language developer tools & local runner

Host: GitHub
URL: https://github.com/chanzuckerberg/miniwdl
Owner: chanzuckerberg
License: mit
Created: 2018-08-11T05:43:50.000Z (over 6 years ago)
Default Branch: main
Last Pushed: 2024-08-14T18:45:46.000Z (5 months ago)
Last Synced: 2024-12-20T07:07:51.763Z (14 days ago)
Topics: wdl, workflow-description-language
Language: Python
Homepage:
Size: 3.15 MB
Stars: 178
Watchers: 14
Forks: 54
Open Issues: 118
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

README

        # miniwdl

**[Workflow Description Language](http://openwdl.org/) local runner & developer toolkit for Python 3.8+**

![Project Status](https://img.shields.io/badge/status-stable-green.svg)

[![MIT license](https://img.shields.io/badge/license-MIT-brightgreen.svg)](https://github.com/chanzuckerberg/miniwdl/blob/main/LICENSE)

[![CI](https://github.com/chanzuckerberg/miniwdl/workflows/CI/badge.svg?branch=main)](https://github.com/chanzuckerberg/miniwdl/actions?query=workflow%3ACI)

[![Coverage Status](https://coveralls.io/repos/github/chanzuckerberg/miniwdl/badge.svg?branch=main)](https://coveralls.io/github/chanzuckerberg/miniwdl?branch=main)

[![Docs Status](https://readthedocs.org/projects/miniwdl/badge/?version=latest)](https://miniwdl.readthedocs.io/en/latest/)

## Install miniwdl

Installation requires Python 3.8+, pip3 (or conda) and Docker (or Podman/Singularity/udocker). Linux preferred; [macOS (Intel) compatible with extra steps](https://github.com/chanzuckerberg/miniwdl/issues/145). More detail in [full documentation](https://miniwdl.readthedocs.io/en/latest/getting_started.html).

- Install with pip [![PyPI version](https://img.shields.io/pypi/v/miniwdl.svg)](https://pypi.org/project/miniwdl/) : run `pip3 install miniwdl`

- Install with conda [![Anaconda-Server Badge](https://anaconda.org/conda-forge/miniwdl/badges/version.svg)](https://anaconda.org/conda-forge/miniwdl) : run `conda install -c conda-forge miniwdl`

- Verify your miniwdl installation: `miniwdl run_self_test`

- Install from source code: see the [Dockerfile](https://github.com/chanzuckerberg/miniwdl/blob/main/Dockerfile) for dependencies to run `setup.py`



## Use miniwdl

Run an example bioinformatics WDL pipeline using miniwdl, or learn more abut miniwdl via a short course (screencast examples).  If you are new to the WDL language, see the open source `learn-wdl` course.  

- [Run an example using a viral genome assembly workflow](https://miniwdl.readthedocs.io/en/latest/getting_started.html)

- [Learn miniwdl course w/screencasts](https://github.com/openwdl/learn-wdl/tree/master/6_miniwdl_course) - shown below

- [Learn WDL course w/screencasts](https://github.com/openwdl/learn-wdl)

[](https://www.youtube.com/playlist?list=PL4Q4HssKcxYv1FQJUD6D1Cu0Q1O-_S1hM)

## [Documentation](https://miniwdl.readthedocs.io/en/latest/WDL.html)

The online documentation includes a user tutorial, reference manual, and Python development codelabs: [![Docs Status](https://readthedocs.org/projects/miniwdl/badge/?version=latest)](https://miniwdl.readthedocs.io/en/latest/WDL.html)

See the [Releases](https://github.com/chanzuckerberg/miniwdl/releases) for change logs. The [Project board](https://github.com/chanzuckerberg/miniwdl/projects/1) shows the current prioritization of [issues](https://github.com/chanzuckerberg/miniwdl/issues).

## Scaling up

The miniwdl runner schedules WDL tasks in parallel up to the CPUs & memory available on the local host; so a more-powerful host enables larger workloads. Separately-maintained projects can distribute tasks to cloud & HPC backends with a shared filesystem:

* AWS:

  * [miniwdl-omics-run](https://github.com/miniwdl-ext/miniwdl-omics-run) tool for the [Amazon Omics](https://aws.amazon.com/omics/) workflow service

  * [AWS Batch plugin](https://github.com/miniwdl-ext/miniwdl-aws) (DIY)

* [SLURM](https://github.com/miniwdl-ext/miniwdl-slurm)

## Getting Help

* [Open an issue](https://github.com/chanzuckerberg/miniwdl/issues)

* [OpenWDL Slack](https://openwdl.slack.com/) (#miniwdl channel)

* [Bioinformatics Stack Exchange](https://bioinformatics.stackexchange.com/questions/tagged/wdl)

## [Contributing](https://github.com/chanzuckerberg/miniwdl/blob/main/CONTRIBUTING.md)

Feedback and contributions to miniwdl are welcome, via issues and pull requests on this repository. See [CONTRIBUTING.md](https://github.com/chanzuckerberg/miniwdl/blob/main/CONTRIBUTING.md) for guidelines and instructions to set up your development environment.

## Security

Please disclose security issues responsibly by contacting [email protected].