Add docs about nextflow_schema.json

CONTRIBUTING.md

@@ -20,11 +20,20 @@ To allow for efficient review, please include in any pull request a concise and
 
 When the changes in `development` merit a new release, a pull request will be filed to merge the current version of the `development` branch into `main`, followed by tagging a release on the `main` branch.
 
+### Updating `nextflow_schema.json`
+
+Any changes that affect the Nextflow configuration files should be reflected in the `nextflow_schema.json` file.
+This file can most easily be updated using the [`nf-core/tools` package](https://nf-co.re/tools), which can be installed with `conda install nf-core`.
+Then run `nf-core schema build` in the `scpca-nf` directory to update the schema file to match the current config file.
+You can also use the web editor that it launches to further customize the schema file.
+Note that you may get warnings about any config parameters that include `${projectDir}`, as the build tool wants those to be replaced with absolute paths.
+This is not necessary for the schema to be valid, so please keep those paths with the `${projectDir}` variable.
+
 ### Continuous integration in pull requests
 
 There are several automatic checks performed by GitHub Actions in all pull requests filed to `main` or `development`:
 
-- [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files. This check is required to pass before pull requests can be merged.
+- [Check Nextflow config](.github/workflows/nextflow-config-check.yaml): This workflow ensures that there are no syntax errors in the Nextflow configuration files and that the `nextflow_schema.json` file is up to date. This check is required to pass before pull requests can be merged.
 - [Check Nextflow stub](.github/workflows/nextflow-stub-check.yaml): This workflow ensures that the [stub workflow](#stub-workflows) runs without errors. This check is required to pass before pull requests can be merged.
 - [Spell check R Markdown and Markdown files](.github/workflows/spell-check.yml): This workflow ensures there are no spelling errors in R Markdown and Markdown files. This check is not required to pass before pull requests can be merged.