rnaseq-nf

RNAseq-NF pipeline for ahab 🦑

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

Build the Docker image

docker build -t tuplexyz/ahab-rnaseq-nf:v1.2.1 .

Running the pipeline in the image locally

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

docker run -v $pwd/data:/mnt/datalake --rm -it --entrypoint bash --name ahab-rnaseq-nf tuplexyz/ahab-rnaseq-nf:v1.2.1

Push to Container Registry

docker push tuplexyz/ahab-rnaseq-nf:v1.2.1

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 rnaseq-nf.yaml

## Bash into a specific node
kubectl exec -it rnaseq-nf-test-00 -- /bin/bash