docs(tutorials): update crypt4GH to proTES guide

[vschnei]

This PR updates the crypt4GH to proTES tutorial guide with important clarifications and branch information for users following the guide.

Changes Made:

• Added a comment explaining how to use a while loop if the Funnel worker terminates after one task execution.

• Added two notes which branches to use during deployment

Summary by Sourcery

Clarify the crypt4gh_to_protes tutorial with additional guidance for running Funnel workers and specifying appropriate proTES and middleware branches during deployment.

Documentation:

• Document how to keep the Funnel worker running continuously using a while loop when it stops after a single task.
• Clarify which proTES and middleware branches to use during deployment when the relevant changes are not yet merged.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Updates the crypt4GH to proTES tutorial with runtime robustness guidance for Funnel workers and clarifies which branches of proTES and its Crypt4GH middleware repositories should be used when following the deployment steps.

Flow diagram for handling Funnel worker termination with while loop

flowchart TD
  A[Start Funnel worker<br/>funnel node run --config worker-config.yaml] --> B{Does worker<br/>terminate after<br/>one task?}
  B -->|No| C[Keep existing<br/>worker command]
  B -->|Yes| D[Wrap command in while loop<br/>while true; do<br/>  funnel node run --config worker-config.yaml<br/>done]
  C --> E[Continue tutorial]
  D --> E

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File-Level Changes

Change	Details	Files
Documented how to keep the Funnel worker running continuously if it exits after a single task.	Added an inline comment in the Funnel setup section explaining that the worker command can be wrapped in a while loop if the worker terminates after executing one task. Provided a commented example of a bash while loop that continuously restarts funnel node run --config worker-config.yaml.	docs/tutorials/crypt4gh_to_protes.md
Clarified which Git branches to use for proTES and its Crypt4GH middleware when following the installation instructions.	Updated the proTES installation instruction to recommend using the adjust_middleware branch if the relevant changes are not yet merged into the default branch. Updated the middleware installation reference to recommend using the update_middleware branch of the protes-middleware-crypt4gh repository if not yet merged.	docs/tutorials/crypt4gh_to_protes.md

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[sourcery-ai]

Hey - I've left some high level feedback:

• Consider clarifying under what exact conditions the Funnel worker terminates and when the while-loop workaround is needed, so users understand why they might need this rather than blindly copying it.
• Instead of embedding specific branch names in the prose, you might want to phrase the instructions so they remain valid after the branches are merged (e.g., note that users should check if the feature is available on the default branch and otherwise use the given branch).

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- Consider clarifying under what exact conditions the Funnel worker terminates and when the while-loop workaround is needed, so users understand why they might need this rather than blindly copying it.
- Instead of embedding specific branch names in the prose, you might want to phrase the instructions so they remain valid after the branches are merged (e.g., note that users should check if the feature is available on the default branch and otherwise use the given branch).

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[Copilot]

Pull request overview

Updates the Crypt4GH → proTES tutorial to reduce user confusion during deployment by adding worker-runtime guidance and specifying which branches to use when upstream changes aren’t merged yet.

Changes:

• Add guidance for keeping a Funnel worker running continuously (while-loop suggestion).
• Clarify which proTES and protes-middleware-crypt4gh branches to deploy when required changes are unmerged.

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