Docs: Move -params-file config from CLI to config (#5534) [ci skip]

Signed-off-by: Christopher Hakkaart <[email protected]>

Author: christopher-hakkaart

docs/cli.md

@@ -243,6 +243,36 @@ $ nextflow run <pipeline> --files "*.fasta"
 ```
 :::
 
+Parameters specified on the command line can be also specified in a params file using the `-params-file` option.
+
+```bash
+nextflow run main.nf -params-file pipeline_params.yml
+```
+
+The `-params-file` option loads parameters for your Nextflow pipeline from a JSON or YAML file. Parameters defined in the file are equivalent to specifying them directly on the command line. For example, instead of specifying parameters on the command line:
+
+```bash
+nextflow run main.nf --alpha 1 --beta foo
+```
+
+Parameters can be represented in YAML format:
+
+```yaml
+alpha: 1
+beta: 'foo'
+```
+
+Or in JSON format:
+
+```json
+{
+  "alpha": 1,
+  "beta": "foo"
+}
+```
+
+The parameters specified in a params file are merged with the resolved configuration. The values provided via a params file overwrite those of the same name in the Nextflow configuration file, but not those specified on the command line.
+
 ## Managing projects
 
 Nextflow seamlessly integrates with popular Git providers, including [BitBucket](http://bitbucket.org/), [GitHub](http://github.com), and [GitLab](http://gitlab.com) for managing Nextflow pipelines as version-controlled Git repositories.

docs/config.md

@@ -138,6 +138,8 @@ params {
 }
 ```
 
+See {ref}`cli-params` for information about how to modify these on the command line.
+
 (config-process)=
 
 ## Process configuration

docs/reference/cli.md

@@ -1172,29 +1172,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
   $ nextflow run main.nf -params-file pipeline_params.yml
   ```
 
-  For example, the following params file in YAML format:
-
-  ```yaml
-  alpha: 1
-  beta: 'foo'
-  ```
-
-  Or in JSON format:
-
-  ```json
-  {
-    "alpha": 1,
-    "beta": "foo"
-  }
-  ```
-
-  Is equivalent to the following command line:
-
-  ```console
-  $ nextflow run main.nf --alpha 1 --beta foo
-  ```
-
-  The parameters specified with this mechanism are merged with the resolved configuration (base configuration and profiles). The values provided via a params file overwrite those of the same name in the Nextflow configuration file.
+  See {ref}`cli-params` for more information about writing custom parameters files.
 
 ### `self-update`