cnv

Callers for copy number variation

💬 Introduction

❗ Dependencies

To run this workflow, the following tools need to be available:

🎒 Preparations

Sample data

1. Add all sample ids to samples.tsv in the column sample.
2. Add all sample data information to units.tsv. Each row represents a fastq file pair with corresponding forward and reverse reads. Also indicate the sample id, run id and lane number, adapter.

Reference data

1. You need a ...

✅ Testing

The workflow repository contains a small test dataset .tests/integration which can be run like so:

cd .tests/integration
snakemake -s ../../Snakefile -j1 --use-singularity

🚀 Usage

The workflow is designed for WGS data meaning huge datasets which require a lot of compute power. For HPC clusters, it is recommended to use a cluster profile and run something like:

snakemake -s /path/to/Snakefile --profile my-awesome-profile

🧑‍⚖️ Rule Graph