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Course summary

Congratulations on completing the Nextflow Run training course! 🎉

Your journey

You started with a very basic workflow, and learned to run it and find its outputs. Then, you ran progressively more realistic versions of that pipeline: processing multiple inputs from a CSV file in parallel, using -resume to skip completed work, and using containers to manage the software a pipeline depends on. Next, you learned how to customize the configuration of a pipeline using nextflow.config and profiles, and how to control where and how its outputs get published. After that, you learned how to generate execution reports, inspect the history of past runs, and clean up old work directories. Finally, you learned how to run pipelines directly from remote repositories such as GitHub.

Skills acquired

Through this hands-on course, you've learned how to:

  • Launch a Nextflow workflow locally and find its outputs
  • Run a multi-step pipeline that processes multiple inputs in parallel
  • Use -resume to avoid repeating completed work
  • Use containers to manage software dependencies
  • Configure pipelines using nextflow.config and profiles
  • Customize where and how outputs get published
  • Generate an HTML execution report with -with-report and an execution timeline with -with-timeline
  • Inspect the history of past runs with nextflow log
  • Clean up old work directories with nextflow clean
  • Run a pipeline directly from a remote repository, and pin it to a specific revision (and unpin it again) for reproducibility

You're now equipped with the foundational knowledge to start integrating existing Nextflow pipelines into your own work.

Next steps to build your skills

Here are our top suggestions for what to do next:

Or, if you're ready to stop just running Nextflow and start writing it, become a Nextflow developer with Hello Nextflow.

Getting help

For help resources and community support, see the Help page.

Feedback survey

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