vg_wdl

Eric T Dawson, Mike Lin and Charles Markello MIT License, 2018

Workflow Description Language (WDL) scripts for common vg workflows

Overview

Docker Containers

WDL needs the runtime Docker image to be present on Dockerhub.
VG images are available in quay and selected images are available in the variantgraphs Dockerhub,
and can be pulled with:

    docker pull variantgraphs/vg  

Specific tags can be specified like so:

# Get the vg 1.3.1 release  
docker pull variantgraphs/vg:1.3.1

Usage

Install miniwdl in a python 3 virtual environment

git clone https://github.com/chanzuckerberg/miniwdl.git
virtualenv miniwdl_venv
source miniwdl_venv/bin/activate
pip3 install ./miniwdl
deactivate

Download .wdl workflow file and .json input file

wget https://github.com/vgteam/vg_wdl/raw/master/workflows/vg_multi_map_call.wdl
wget https://github.com/vgteam/vg_wdl/raw/master/params/vg_multi_map_call.inputs_tiny.http_url.json

Activate the miniwdl virtual environment and run the example workflow

source miniwdl_venv/bin/activate
miniwdl cromwell vg_multi_map_call.wdl -i vg_multi_map_call.inputs_tiny.http_url.json

To modify the input parameters, edit the input .json with the necessary changes.

Examples

Availability

Workflow for processing single sample datasets:

• workflow file
• parameter file
• Dockstore page

Workflow for processing pedigree datasets:

• workflow file
• parameter file

Workflow for mapping and calling structural variants in a single sample:

• workflow file
• parameter file
• Dockstore page

Contributing, Help, Bugs and Requests

Please open an Issue on github for help, bug reports, or feature requests. When doing so, please remember that vg_wdl is open-source software made by a community of developers. Please be considerate and support a positive environment.