MobiDL

MobidicWDL workflows

Goals

Providing wdl workflows to treat NGS data

Repos architecture and requirements

• Each step can be found in dedicated wdls in modules/

• A workflow imports individual wdls and run them, see panelCapture.wdl for details

• json files are provided as examples

• needs crowmwell to run

• see requirements file for a complete list of software that need to be installed

Validate a workflow

• requires womtools

java -jar /PATH/TO/womtool.jar validate panelCapture.wdl 

Run

java -jar /PATH/TO/cromwell.jar run panelCapture.wdl -i panelCapture_inputs.json

Workflow captainAchab

The best way to run this workflow is by using the singularity container. You will find documentation about MPA and Achab here and here.

Workflow panelCapture

This workflow is dedicated to NGS experiments based on capture libraries, and focusing on gene panels/exomes. It uses GATK 4 Haplotype Caller and google DeepVariant for variant calling. Alignment output is a crumbled CRAM file.

This workflow requires as input 2 fastqs and one ROI bed file.

All software paths and input paths are to be modified in the json file (example: panelCapture_example_inputs.json). All paths are absolute, except for deepvariant paths. Indeed, DeepVariant is used in MobiDL as a singularity container, then input (Fastqs, ROI bed file) and output paths need to be bound. Inside the container, the path to bound folders is '/dv2'. The DeepVariant singularity container has been built using this link See also the changelog file.