Welcome to Janis workshop. This is a 2-part workshop where we will use Janis to build a genomic variant-calling pipeline.
Workflows from this workshop are adopted from the following GATK (Broad Institute)'s WDL pipelines with modifications to simplify the tasks for the purpose of this workshop.
- https://github.com/gatk-workflows/gatk4-data-processing
- https://github.com/gatk-workflows/gatk4-germline-snps-indels
The goal of this workshop is to introduce Janis for building portable pipelines. We build a toy variant-caller that works for small data sets. Please note that the pipeline produced by this workshop should only be used as a guide, and is NOT for production usage. Please consider reviewing the pipeline details such as tools' parameters, genome references and databases at the end of this workshop if you are intend to use this for other samples.
- Janis Documentation: https://janis.readthedocs.io/en/latest
- Janis GitHub: https://github.com/PMCC-BioinformaticsCore/janis
- This workshop GitHub: https://github.com/PMCC-BioinformaticsCore/janis-training
For the first session, we will get ourselves familiar with Janis.
| Description | |
|---|---|
| 30 minutes | Introduction to Janis - Installing and setting up Janis Environment - Running a small workflow as a test |
| 30 minutes | Building a workflow to align a set of fastqs - Learn about preconfigured tools - Using BWA mem + samtools view - Add Mark Duplicates - Running a small test |
| 30 minutes | Exercise: Extend alignment to complete data processing - Add SortSam + SetNmMdAndUqTags - Test the pipeline |
For the second session, we will complete our portable germline variant-calling pipeline
| Description | |
|---|---|
| 30 minutes | Adding new tools definition in Janis - Create Janis' GATK ApplyBQSR + GATK BaseRecalibrator - Add new tools to workflow - Test updated pipeline |
| 30 minutes | Exercise: Adding more tools to complete germline pipeline - Add GATK HaplotypeCaller - Add new tool to workflow - Test updated pipeline |
| 30 minutes | Wrap-up - Going through exercise' solutions - Q&A |
Prerequisites to install Janis on your personal computer:
- A unix-based operating system (MacOS / Ubuntu / RHEL / CentOS / etc)
- Python 3.6+
- Docker
- Zip (archiver for zip files)
- Node.js