Variant Calling

Tutorial Overview

Before constructing a nextflow workflow, it is imperative to understand what files are required and produced by each step. We will run the analysis in an interactive shell stepping through each phase of the pipeline before moving to nextflow scripting.

The tutorial will be composed of:

1. Work through the pipeline ~1 hour
2. Reusable channels in nextflow ~20 min
3. Alignment, Mark Duplicates exercise ~40 min
4. Execute full nextflow script