Parabricks WDL

This is a repository of WDL workflow files for popular Parabricks tools.

Table of Contents

• Quick Start
• Full Tutorial
  • Install Sprocket
  • Run the tests
• Future Work

Quick Start

To get up and running with this repository as quickly as possible, use the commands below.

# Clone the repo and cd into directory 
git clone https://github.com/clara-parabricks-workflows/Parabricks-WDL-Workflows.git
cd parabricks-wdl

# Install Sprocket
curl https://sh.rustup.rs -sSf | sh
cargo install sprocket --locked

# Download all the test data 
make 

# Run the full test suite  
sprocket dev test

Full Tutorial

Install Sprocket

Install Rust using rustup. This will also install Cargo, the Rust package manager

curl https://sh.rustup.rs -sSf | sh

Install Sprocket using Cargo

cargo install sprocket --locked

Hint: If OpenSSL issues arise, then users may need to run sudo apt install libssl-dev

Download the test data

To download all the test data run:

make

To download data just for one test, just append the directory name:

make fq2bam

Run the tests

This repo uses the Sprocket unit testing framework. See the documentation for more information.

To run the full test suite use:

sprocket dev test

To run a specific test specify the root directory with -w and provide the directory name. See the fq2bam example below:

sprocket dev test -w . fq2bam

Future Work

• Add CI to repo