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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, find the outputs, and manage its execution. Then, you worked your way through increasingly more complex versions of that workflow and learned to recognize the essential concepts and mechanisms that power Nextflow pipelines, including channels and operators, code modularization, and containers. Finally, you learned how to customize the configuration of a pipeline to fit your preferences and your computational infrastructure.

What you learned

You are now able to manage the execution of the Hello pipeline, describe how it is structured, and identify the main pieces of code involved.

  • The final form of the Hello workflow takes as input a CSV file containing text greetings.
  • The four steps are implemented as Nextflow processes (sayHello, convertToUpper, collectGreetings, and cowpy) stored in separate module files.
  • The results are published to a directory called results/.
  • The final output of the pipeline is a plain text file containing ASCII art of a character saying the uppercased greetings.
sayHello*-output.txtconvertToUpperUPPER-*collectGreetingsCOLLECTED-output.txtHELLOBONJOURHOLàHello,English,123 Bonjour,French,456Holà,Spanish,789greetings.csvHELLOBONJOURHOLàUPPER-Hello-output.txtUPPER-Bonjour-output.txtUPPER-Holà-output.txtcowPycowpy-COLLECTED-output.txt ________/ HOLà \| HELLO |\ BONJOUR / -------- \ ^__^ \ (oo)\_______ (__)\ )\/\ ||----w | || ||
  1. sayHello: Writes each greeting to its own output file (e.g. "Hello-output.txt")
  2. convertToUpper: Converts each greeting to uppercase (e.g. "HELLO")
  3. collectGreetings: Collects all uppercase greetings into a single batch file
  4. cowpy: Generates ASCII art using the cowpy tool

The workflow configuration supports providing inputs and parameters in a flexible, reproducible way.

Skills acquired

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

  • Launch a Nextflow workflow locally
  • Find and interpret outputs (results) and log files generated by Nextflow
  • Recognize the core Nextflow components that constitute a simple multi-step workflow
  • Describe next-step concepts such as operators and channel factories
  • Troubleshoot basic issues

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 3 suggestions for what to do next:

Finally, we recommend you have a look at Seqera Platform, a cloud-based platform developed by the creators of Nextflow that makes it even easier to launch and manage your workflows, as well as manage your data and run analyses interactively in any environment.

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