콘텐츠로 이동

Course summary

Translation in Progress

This page has not yet been translated into your language. You are viewing the original English content.

Want to help? See our translation guide.

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

Your journey

You started by finding and retrieving the nf-core/demo pipeline, then learned to run it using its test profile and examine its outputs. Next, you configured its execution through pipeline parameters and configuration files, and saw how nf-core pipelines validate parameters and input data. Finally, you applied those same skills to nf-core/rnaseq, a production-scale pipeline, and learned how to override its default resource allocations to fit the hardware available to you.

What you learned

You are now able to find, retrieve, run, and configure nf-core pipelines.

  • nf-core pipelines are retrieved with nextflow pull and follow a standard code organization.
  • Every nf-core pipeline ships with a test profile for quick validation on a small dataset.
  • Pipeline parameters (set via --param_name or -params-file) and configuration (set via -c) serve different purposes: inputs and analysis options versus execution logistics like resource allocation.
  • nf-core pipelines validate parameters and input files automatically, catching errors before any work is done.
  • Resource defaults are assigned through labels (process_low, process_medium, process_high) defined in conf/base.config, which you can override with a custom configuration file.

Skills acquired

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

  • Find an nf-core pipeline on the nf-co.re website and retrieve its source code
  • Run a pipeline using its built-in test profile and examine its outputs
  • Get help, set parameters, and understand parameter and input validation
  • Customize resource allocation and tool arguments through configuration files
  • Pull and run a production-scale pipeline, and override its default resource labels

You're now equipped with the foundational knowledge to start running nf-core pipelines for your own analyses.

Next steps to build your skills

Here are our top suggestions for what to do next:

  • Don't just run nf-core pipelines, develop them! Learn nf-core best practices with Hello nf-core
  • New to Nextflow itself? Start with Nextflow Run
  • Apply Nextflow to a scientific analysis use case with Nextflow for Science
  • Explore more advanced Nextflow features with the Side Quests

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.

Getting help

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

Feedback survey

Before you move on, please take a minute to complete the course survey! Your feedback helps us improve our training materials for everyone.

Take the survey