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Creating schema files

Warning

It's highly recommended that you don't try to write the schema JSON file manually!

The schema files can get large and complex and are difficult to debug. Don't be tempted to open in your code editor - instead use the provided tools!

Requirements

To work with Nextflow schema files, you need the nf-core command-line tools package. You can find full installation instructions in the nf-core documentation, but in brief, you install as with any other Python package:

pip install nf-core
# -- OR -- #
conda install nf-core # (1)!
  1. ⚠ Note: Needs bioconda channels to be configured! See the Bioconda usage docs.

Info

Although these tools are currently within the nf-core tooling ecosystem, they should work with any Nextflow pipeline: you don't have to be using the nf-core template for this.

Note

We aim to extract this functionality into stand-alone tools at a future date, as we have done with the pipeline validation code in this plugin.

Build a pipeline schema

Once you have nf-core/tools installed and have written your pipeline configuration, go to the pipeline root and run the following:

nf-core schema build

The tool will run the nextflow config command to extract your pipeline's configuration and compare the output to your nextflow_schema.json file (if it exists). It will prompt you to update the schema file with any changes, then it will ask if you wish to edit the schema using the web interface.

This web interface is where you should add detail to your schema, customising the various fields for each parameter.

Tip

You can run the nf-core schema build command again and again, as many times as you like. It's designed both for initial creation but also future updates of the schema file.

It's a good idea to "save little and often" by clicking Finished and saving your work locally, then running the command again to continue.

Build a sample sheet schema

Danger

There is currently no tooling to help you write sample sheet schema 😧

Watch this space..