modify index files

Author: Sven Twardziok

docs/general/index.md

@@ -5,14 +5,10 @@ This section provides the cross-cutting context for the ELIXIR-on-Cloud ecosyste
 ## In this section
 
 - [GA4GH Cloud Workstream](ga4gh_cloud.md)
-	Introduces the GA4GH cloud APIs that enable interoperable, federated analysis across providers. It gives background and examples for core standards used throughout this documentation (WES, TES, DRS, TRS) and how they fit into real workflows.
+  Introduces the GA4GH cloud APIs that enable interoperable, federated analysis across providers. It gives background and examples for core standards used throughout this documentation (WES, TES, DRS, TRS) and how they fit into real workflows.
 
 - [Processing Sensitive Data](sensitive_data.md)
-	Summarizes key requirements and scenarios for working with sensitive human data in cloud contexts, including relevant legal/regulatory frameworks (e.g., GDPR, EHDS) and typical secure analysis environments (TEE/SPE/TRE).
+  Summarizes key requirements and scenarios for working with sensitive human data in cloud contexts, including relevant legal/regulatory frameworks (e.g., GDPR, EHDS) and typical secure analysis environments (TEE/SPE/TRE).
 
 - [User Stories](user_stories.md)
-	Collects user stories that describe common journeys (access to services, access to data, and running analyses). Use these to align expectations between researchers, service providers, and data controllers.
-
-## Where to go next
-
-If you are new to the project, start with the user stories to get an end-to-end picture, then dive into the GA4GH overview for the technical standards. If you handle human data (or build platforms that do), read the sensitive data page early to avoid design decisions that conflict with governance and compliance requirements.
+  Collects user stories that describe common journeys (access to services, access to data, and running analyses). Use these to align expectations between researchers, service providers, and data controllers.

docs/tutorials/index.md

@@ -0,0 +1,11 @@
+# Tutorials
+
+This section contains hands-on, end-to-end tutorials that show how to deploy and use components of the ELIXIR-on-Cloud ecosystem. The guides are written to be actionable: they focus on concrete setups, expected infrastructure, and the sequence of steps needed to run secure analyses.
+
+## In this section
+
+- [Crypt4GH Integration with proTES](crypt4gh_to_protes.md)
+  Shows a pattern for analyzing encrypted genomic data in the cloud without granting researchers direct access to the plaintext. It combines Crypt4GH encryption with GA4GH TES execution via Funnel and proTES, including automatic decryption inside controlled containers.
+
+- [Analysis of Sensitive Data in Secure Processing Environments (SPE)](sensitive_data_analysis.md)
+  Walks through a reference setup for an SPE (example: de.NBI Cloud / ELIXIR-DE) using WESkit for workflow submission, a Slurm cluster for execution, and S3-compatible storage for publishing non-sensitive results. It also outlines how LS Login can be used for authentication and authorization.