Eric T Dawson, Mike Lin and Charles Markello MIT License, 2018
Workflow Description Language (WDL) scripts for common vg workflows
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
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.
Workflow for processing single sample datasets:
Workflow for processing pedigree datasets:
Workflow for mapping and calling structural variants in a single sample:
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.