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Hands-on 4: Reproducible pipelines with containers

Question

  1. Run the Nextflow pipeline with the docker provider and generate the results
curl -s https://get.nextflow.io | bash
 ./nextflow run nextflow-io/rnaseq-nf -with-docker
  1. Use a caddy server to serve results on port 8888
docker run -d -p 8888:80 -v "$PWD/results/multiqc_report.html:/usr/share/caddy/index.html" caddy

Solution

  • All the steps are in the Makefile
  • Use make solution to make all the steps.