feat: add profile info

[cmeesters]

Snakemake workflows to be executed on cluster or cloud environments deployed with snakedeploy meanwhile copy a profiles directory, if present.

This PR attempts to add an empty profiles directory. It includes a brief description in the README.md and adds a similar file in the profiles directory.

Summary by CodeRabbit

• Documentation
  • Added a new guide explaining how to organize cluster- and cloud-specific workflow profiles.
  • Documented the recommended directory layout and where configuration files for each target should live.
  • Provided guidance for contributors to add third-party profiles and for noting workflow-specific considerations.
  • Included optional guidance for marking rules used only in local/server-focused development.

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📥 Commits

Reviewing files that changed from the base of the PR and between 04f13c0 and 014867f.

📒 Files selected for processing (1)

• README.md (2 hunks)

Walkthrough

Adds documentation describing the recommended profiles directory layout and usage: a new "The 'profiles' Directory" section in README.md and a new profiles/README.txt explaining per-cluster/cloud profiles/<name>/config.yaml, optional adjacent READMEs, contribution guidance, and local-rules guidance.

Changes

Cohort / File(s)	Summary
Root README update README.md	Added "The 'profiles' Directory" section describing placement and purpose of profiles/<cluster or cloud name>/config.yaml and optional adjacent README for considerations.
Profiles documentation added profiles/README.txt	New file documenting purpose, recommended layout (profiles/<your cluster or cloud instance>/config.yaml), optional readme for pitfalls, community contribution guidance, and optional localrules directive guidance.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

• Documentation-only changes; no code or API surface modified.
• Review focus: clarity and accuracy of instructions in profiles/README.txt and the new README section.

Poem

🐰 In a burrow of files I nibble and write,
Profiles in rows, each cluster sleeps tight.
Configs tucked neat in a soft YAML nest,
Contributors hop in to help do their best.
Pipelines hum on, well-guided and bright. ✨

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The PR title "feat: add profile info" is directly related to the main changes in the pull request. The changeset adds documentation about the profiles directory in README.md and introduces a new profiles/README.txt file that describes the structure and purpose of profiles for cluster or cloud configurations. The title accurately conveys that profile-related information is being added to the repository. While the title could be slightly more specific about documenting profiles for cluster/cloud execution, it is clear enough that a teammate reviewing the history would understand the primary change.

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[coderabbitai]

Actionable comments posted: 2

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between c7bb8f6 and a1b6b49.

📒 Files selected for processing (2)

• README.md (1 hunks)
• profiles/README.txt (1 hunks)

🧰 Additional context used

🪛 LanguageTool

profiles/README.txt

[style] ~8-~8: Consider using a less common alternative to make your writing sound more unique and professional.
Context: ... pitfalls or other things to consider. Feel free to open pull requests for 3rd party workfl...

(FEEL_FREE_TO_STYLE_ME)

---

[grammar] ~9-~9: Use a hyphen to join words.
Context: ... Feel free to open pull requests for 3rd party workflows you are working with to ...

(QB_NEW_EN_HYPHEN)

---

[grammar] ~9-~9: Ensure spelling is correct
Context: ...n during development, e.g. plotting and dowload rules.

(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)

README.md

[grammar] ~59-~59: Ensure spelling is correct
Context: ...cular execution environment (cluster or cload). You may include a readme file next to...

(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)

[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

README.md (1)

10-15: Add the new section to the table of contents.

The "The 'profiles' Directory" section should be added to the table of contents for consistency and to help users navigate the documentation.

Apply this diff to update the table of contents:

 - [Snakemake workflow: `<name>`](#snakemake-workflow-name)
   - [Usage](#usage)
   - [Deployment options](#deployment-options)
+  - [The 'profiles' Directory](#the-profiles-directory)
   - [Authors](#authors)
   - [References](#references)
   - [TODO](#todo)

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between a1b6b49 and 04f13c0.

📒 Files selected for processing (2)

• README.md (1 hunks)
• profiles/README.txt (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• profiles/README.txt

🔇 Additional comments (1)

README.md (1)

53-59: Good typo fix and clear documentation.

The spelling error flagged in the previous review ("cload" → "cloud") has been corrected, and the new section provides clear guidance on the profiles directory structure and purpose.

[m-jahn]

Hi Christian, great idea to include profiles!
I have some general comments that could be addressed to make this even more user-friendly:

• maybe change the README.txt to a README.md in line with all other markdown docs we use for documentation? This would also include the file in automatic md linting by Github actions
• would you like to include an actual dummy profile? Or would that conflict with other parts of a workflow template? From my point of view that would be OK since profile will stay silent until it is invoked with snakemake --profile right? If we like to encourage the use of profiles, a real working profile including a statement how to invoke it would be a really cool addition.

[m-jahn]

directory lower-case

[m-jahn]

directory lower-case

[m-jahn]

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

[cmeesters]

@m-jahn will switch to lower case and add a template for this particular workflow. Will only able to do this by the end of the week.

[m-jahn]

thanks for doing this!