Workflow : GATK-best-practices-RNA

This workflow do VariantCalling on Illumina RNA sequencing data.

Installation

Clone the repo

git clone --recursive https://github.com/MobiDL/GATK-BP-RNA.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 GATK-best-practices-RNA

Configure your inputs

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

Minimal

{
	"GATK_best_practices_RNA.fastqR1": "File",
	"GATK_best_practices_RNA.fastqR2": "File? (optional)",
	"GATK_best_practices_RNA.dbsnp": "File",
	"GATK_best_practices_RNA.dbsnpIdx": "File",
	"GATK_best_practices_RNA.knownSites": "Array[File]",
	"GATK_best_practices_RNA.knownSitesIdx": "Array[File]",
	"GATK_best_practices_RNA.genomeDir": "File",
	"GATK_best_practices_RNA.outputPath": "String",
	"GATK_best_practices_RNA.refDict": "File",
	"GATK_best_practices_RNA.refFai": "File",
	"GATK_best_practices_RNA.refFasta": "File",
}

Extended

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

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 GATK-best-practices-RNA
cromwell run \
	-Dconfig.file=backends.conf/local.conf \
	--inputs /path/to/inputs.json \
	GATK-BP-RNA.wdl