micro-c

Overview

WDL implementation of Dovetail micro-c analysis pipeline.

Installation

1. Git clone this repository

$ git clone https://github.com/miller-alexander/micro-c

2. Install Cromwell

Follow this guide

3. Configure Cromwell for use with your compute framework

Note: Configuration requires runtime attributes Int cpu, Int memory_gb, String jobGroup, and String docker.

Usage

1. Generate the input json

See Generate_Inputs.MD for information on how to generate inputs.

2. Launch the WDL with Cromwell

$ java -Dconfig.file=backend.conf -jar cromwell.jar run -t wdl -m outfile.json -i inputs.json micro_c.wdl