Course summary¶

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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