wgs-tutorial

WGS pipeline for ahab 🦑

This pipeline is based on the example wgs-tutorial pipeline with modifications to run in the ahab system.

Build the Docker image

docker build -t tuplexyz/ahab-snakemake-wgs-tutorial:v8.13.0 .

Running the pipeline in the image locally

(Using a volume to simulate the data lake connection.)

docker run -v $pwd/data:/mnt/datalake/samples/wgs-tutorial/ --rm -it --entrypoint bash --name ahab-snakemake-wgs-tutorial tuplexyz/ahab-snakemake-wgs-tutorial:v8.13.0

Push to Container Registry

docker push tuplexyz/ahab-snakemake-wgs-tutorial:v8.13.0

Applying a pod manually for testing

## Login to Azure and get AKS credentials
az login
az aks get-credentials --resource-group <Resource Group> --name <AKS Name> --overwrite-existing
# az aks get-credentials --resource-group rg-ahab-dev-eastus-001 --name kub-ahab-dev-eastus-001 --overwrite-existing

## Apply YAML
kubectl apply -f wgs-snakemake.yaml

## Bash into a specific node
kubectl exec -it wgs-snakemake-test-00 -- /bin/bash