Workshop Nextflow

Running with Docker

Use this command if nextflow is not installed and you want to use the official docker image

alias nextflow="docker run --rm -it \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v $(pwd):/$(pwd) -w $(pwd) nextflow/nextflow:24.04.4 nextflow"

Prepare data

Change directory where this project is located, do not enter this project's directory. To generate dummy data, run

ws-nextflow/generate_data.sh ./data

You should see the data directory beside the ws-directory

$ ls
drwxr-xr-x@  7 user  user   224B 22 Oct 16:16 data
drwxr-xr-x@  8 user  user   256B 18 Oct 23:45 ws-nextflow

Run the workflow

nextflow run ws-nextflow --data ./data --output results