Chapter1 gives an overview of different bioinformatics workflows.
In this repository, variant calling is described using different workflows such as GNU Make, Snakemake and Ruffus.
All workflows use
- data in
datadirectory - reference in
refsdirectory - config file and sample sheet in
configfolder.
The code for each workflow is in src under each workflow name.
For example, snakemake variant calling workflow can be invoked as
snakemake -s src/snakemake/variants.smk
Variant calling workflows included here are.