Nextflow Hello World (GitHub Actions)

A minimal project that runs a Nextflow "Hello World" pipeline on every push to main (limited to changes in pipelines/hello/** or the workflow file).

Structure

pipelines/
  hello/
    main.nf          # Hello pipeline (DSL2)
.github/
  workflows/
    hello-on-push.yml  # CI workflow that installs Nextflow and runs the pipeline
nextflow.config        # optional local profile

How it works

1. GitHub Actions sets up Java 17 and installs Nextflow.
2. Runs: nextflow run pipelines/hello -profile local.
3. Publishes artifacts: report.html, timeline.html, trace.txt, and hello.txt.

Quick local test

nextflow run pipelines/hello -profile local
cat hello.txt

Notes

• No secrets or cluster required. This uses the local executor on GitHub-hosted runners.
• You can later replace the run step with an Argo submit to execute in your cluster.