Workflow : ONT-VariantCalling

This workflow do VariantCalling on Oxford Nanopore Technologies data.

Installation

Clone the repo

git clone --recursive https://github.com/MobiDL/ONT-VariantCalling.git

Install dependencies

Conda is recommended: see here to install conda

You will need to create a new environment based on conda.

conda env create -f environment.yml
conda activate ONT-VariantCalling

Following specifications on Clair, you will need to install intervaltree package :

pypy3 -m ensurepip
pypy3 -m pip install --no-cache-dir intervaltree==3.0.2
conda deactivate

Configure your inputs

You can create your input file replacing editing the template or creating your own inputs file.

Minimal

{
	"ONT_VariantCalling.fastqPath": "String",
	"ONT_VariantCalling.refFa": "File",
	"ONT_VariantCalling.refFai": "File",
	"ONT_VariantCalling.modelPath": "String",
	"ONT_VariantCalling.outputPath": "String",
}

Extended

A full option templates is provided (inputs.tpl.json).

This template is separating in 4 categories (blank line) :

1. Global pipeline inputs (i.e. minimal)
2. Global pipeline options
3. Specific tasks inputs
4. Specific tasks options

Launch

Local

conda activate ONT-VariantCalling
cromwell run \
	-Dconfig.file=backends.conf/local.conf \
	--inputs /path/to/inputs.json \
	ONT-VariantCalling.wdl