Update nf_core/pipeline-template/docs/usage.md

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

nf_core/pipeline-template/docs/usage.md

@@ -79,7 +79,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) and other infrastructural tweaks.
+> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 > The above pipeline run specified with a params file in yaml format:
 
 ```bash