Merge pull request #2173 from nf-core/params-file-docs2

Add params file docs to usage.md in template

CHANGELOG.md

@@ -4,7 +4,8 @@
 
 ### Template
 
-- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163))
+- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133]
+- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub]
 
 ### Linting
 

nf_core/pipeline-template/docs/usage.md

@@ -75,6 +75,29 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
+
+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), other infrastructural tweaks (such as output directories), or module arguments (args).
+> The above pipeline run specified with a params file in yaml format:
+
+```bash
+nextflow run {{ name }} -profile docker -params-file params.yaml
+```
+
+with `params.yaml` containing:
+
+```yaml
+input: './samplesheet.csv'
+outdir: './results/'
+genome: 'GRCh37'
+input: 'data'
+<...>
+```
+
+You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
@@ -91,6 +114,10 @@ First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releas
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
+To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+
+> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+
 ## Core Nextflow arguments
 
 > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).