feat: add profile info

README.md

@@ -10,6 +10,7 @@ A Snakemake workflow for `<description>`
 - [Snakemake workflow: `<name>`](#snakemake-workflow-name)
   - [Usage](#usage)
   - [Deployment options](#deployment-options)
+  - [Workflow profiles](#workflow-profiles)
   - [Authors](#authors)
   - [References](#references)
   - [TODO](#todo)
@@ -50,6 +51,11 @@ Run the workflow with:
 snakemake --cores 2 --sdm conda apptainer --directory .test
 ```
 
+## Workflow profiles
+
+The `profiles/` directory can contain any number of [workflow-specific profiles](https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles) that users can choose from.
+The [profiles `README.md`](profiles/README.md) provides more details.
+
 ## Authors
 
 - Firstname Lastname

profiles/README.md

@@ -0,0 +1,17 @@
+The `profiles/` directory can contain any number of subdirectories, each containing a `config.yaml` file with a [workflow-specific profile](https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles):
+
+`profiles/<specific_profile_name>/config.yaml`
+
+The profile `profiles/default/config.yaml` will automatically be used by snakemake whenever you don't provide a workflow-specific profile via `--workflow-profile`.
+This means that any resources or other (command line) arguments specified there, will implicitly be used when running this workflow.
+Thus, as a workflow developer, only put configurations there that you expect to work in most environments, but which the users might want to tweak.
+And for rule-specific resource setting, preferably provide generally applicable settings right in the rule definition, if necessary via [dynamic resource](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#dynamic-resources) specification---users can always override those in a profile, if they need to.
+
+For any more specific profiles, use separate and clearly named subdirectories.
+For example use `profiles/slurm/config.yaml` for a slurm-specific profile, or even something like `profiles/slurm_uni_xyz/config.yaml` for a particular institutional slurm compute cluster.
+
+It is also good practice to add clear documentation comments for each entry in a (workflow) profile.
+This should explain the respective entry, indicate what kind of values can be used and why a particular value or setting were chosen.
+To this end, it is often helpful to provide links to relevant documentation pages, either from snakemake, a snakemake plugin or a specific cluster environment.
+
+In general, we welcome pull requests for 3rd-party workflows you are working with to include such a profile for your specific compute environment.