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Course summary

Congratulations on completing the Hello Nextflow training course! 🎉

See the whole playlist on the Nextflow YouTube channel.

📗 You can read the video transcript alongside the video.

Your journey

You started with a very basic workflow that ran a hardcoded command. Over the course of six parts, you transformed that basic workflow into a modular multi-step pipeline that exercises key features of Nextflow including channels, operators, built-in support for containers, and configuration options.

What you built

  • 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:

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

You're now equipped with the foundational knowledge to start developing your own pipelines in Nextflow.

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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