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feat: add profile info #20

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d0a8ea2
feat: added profiles directory with a README.txt
cmeesters Oct 26, 2025
a1b6b49
feat: included information to the profiles directory
cmeesters Oct 26, 2025
73e9dc2
Update profiles/README.txt
cmeesters Oct 26, 2025
04f13c0
Update README.md
cmeesters Oct 26, 2025
014867f
fix: added missing content section
cmeesters Oct 26, 2025
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9 changes: 9 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ A Snakemake workflow for `<description>`
- [Snakemake workflow: `<name>`](#snakemake-workflow-name)
- [Usage](#usage)
- [Deployment options](#deployment-options)
- [The "profiles" Directory](#the-profiles-directory)
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@m-jahn m-jahn Oct 26, 2025

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directory lower-case

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@dlaehnemann dlaehnemann Jan 14, 2026

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- [The "profiles" Directory](#the-profiles-directory)
- [Workflow profiles](#workflow-profiles)

- [Authors](#authors)
- [References](#references)
- [TODO](#todo)
Expand Down Expand Up @@ -50,6 +51,14 @@ Run the workflow with:
snakemake --cores 2 --sdm conda apptainer --directory .test
```

## The "profiles" Directory
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directory lower-case

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@dlaehnemann dlaehnemann Jan 14, 2026

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## The "profiles" Directory
## Workflow profiles


When developing on a cluster or cloud instance, please include a "profiles" directory:

`profiles/<cluster or cloud name>/config.yaml`

This configuration file should contain the workflow profile with its resource specification for a particular execution environment (cluster or cloud). You may include a readme file next to point out pitfalls or other aspects worth a user's consideration.
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@dlaehnemann dlaehnemann Jan 14, 2026

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When developing on a cluster or cloud instance, please include a "profiles" directory:
`profiles/<cluster or cloud name>/config.yaml`
This configuration file should contain the workflow profile with its resource specification for a particular execution environment (cluster or cloud). You may include a readme file next to point out pitfalls or other aspects worth a user's consideration.
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
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9 changes: 9 additions & 0 deletions profiles/README.txt
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@@ -0,0 +1,9 @@
A 'profiles' directory might contain workflow resource configuration for a particular cluster or cloud instance.

We encourage to include a profile for your use case as:

`profiles/<your cluster or cloud instance>/config.yaml`

You may include a readme file next to the config.yaml file to point out pitfalls or other things to consider.
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@m-jahn m-jahn Oct 26, 2025

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You may include a README.md file [...]


We welcome pull requests for 3rd-party workflows you are working with to include such a profile! It may also be necessary to occasionally label certain rules of a particular workflow with the `localrules: <rule 1>, <rule 2>, ...` directive when workflow developers focused on server execution during development, e.g., plotting and download rules.
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@dlaehnemann dlaehnemann Jan 14, 2026

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A 'profiles' directory might contain workflow resource configuration for a particular cluster or cloud instance.
We encourage to include a profile for your use case as:
`profiles/<your cluster or cloud instance>/config.yaml`
You may include a readme file next to the config.yaml file to point out pitfalls or other things to consider.
We welcome pull requests for 3rd-party workflows you are working with to include such a profile! It may also be necessary to occasionally label certain rules of a particular workflow with the `localrules: <rule 1>, <rule 2>, ...` directive when workflow developers focused on server execution during development, e.g., plotting and download rules.
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.

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