Docker container

The pipline needs the following tools:

• Picard Tools

• Genome Analysis Toolkit (GATK)

• STAR - RNA mapper

• samtools

• R

A Docker container with all tools except the Genome Analysis Toolkit can be built from the Dockerfile present in this folder.

A prebuilt Docker container is available at the Docker hub as cbcrg/ngs2017ws-nf.

For the Genome Analysis Toolkit we use biodckrdev/gatk available at the Docker hub.