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Course summary

Congratulations on completing the Hello nf-core training course! 🎉

Your journey

You started by learning retrieve and run a demo pipeline, then tackled the conversion of a simple Nextflow workflow into an nf-core pipeline. You learned how to create a pipeline scaffold using a template and grafted the existing pipeline onto that scaffold. Then you gradually refined the pipeline by replacing one of the local modules with an nf-core module, transformed another one of the local modules to fit nf-core standards, and added input validation.

What you built

Your final core-hello pipeline now has:

  • Standardized structure using the nf-core template with organized directories for workflows, subworkflows, modules, and configuration
  • Community modules from the nf-core repository (cat/cat) alongside your custom modules
  • Comprehensive validation that checks both parameters and input data before the pipeline runs
  • Professional configuration with profiles for different execution environments
  • Complete documentation and metadata following nf-core conventions

Key skills acquired

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

  1. Navigate and understand nf-core pipeline structure by exploring an existing pipeline
  2. Restructure workflows to be composable and fit within the nf-core template
  3. Find and integrate pre-built modules from the community repository
  4. Create custom modules following nf-core standards for naming, structure, and metadata
  5. Implement validation using nf-schema to catch errors early with clear feedback

You're now equipped with the foundational knowledge to build production-ready nf-core pipelines that follow community best practices.

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.

Feedback survey

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