- Rename conf/uppmax/uppmax.config to conf/uppmax/nextflow.config
- Rename conf/uppmax/pipeline/ to conf/uppmax/pipelines/
- Move pipeline-specific configs to their own subdirectories:
  - conf/pipeline/sarek/uppmax.config → conf/uppmax/pipelines/sarek/nextflow.config
  - conf/pipeline/ampliseq/uppmax.config → conf/uppmax/pipelines/ampliseq/nextflow.config
- Move pipeline documentation to co-located README files:
  - docs/pipeline/sarek/uppmax.md → conf/uppmax/pipelines/sarek/README.md
  - docs/pipeline/ampliseq/uppmax.md → conf/uppmax/pipelines/ampliseq/README.md
- Remove duplicate config and documentation files

All uppmax-related files are now co-located under conf/uppmax/ with
consistent naming conventions (nextflow.config, README.md).

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Update the includeConfig path for uppmax profile to point to the new
location at conf/uppmax/nextflow.config after directory reorganization.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Add bin/reorganize-cluster.sh script to automate the reorganization
of cluster configuration directories to follow the new structure:

- Renames cluster.config → nextflow.config
- Renames pipeline/ → pipelines/
- Moves pipeline configs to organized subdirectories
- Moves pipeline docs to co-located README files
- Updates nfcore_custom.config with correct paths
- Provides comprehensive logging and validation

Usage: ./bin/reorganize-cluster.sh <cluster_name>

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

- Reorganize sanger cluster configuration to new directory structure:
  - conf/sanger.config → conf/sanger/nextflow.config
  - Update nfcore_custom.config path reference
- Improve reorganize-cluster.sh script to handle single config files:
  - Create cluster directory if it doesn't exist
  - Move standalone .config files into directory structure
  - Support both existing directories and single files

This demonstrates the automation working for the common case where
clusters have a single config file rather than a complex directory.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Add comprehensive documentation to CLAUDE.md covering:

- New directory structure pattern with examples
- Automated migration process using reorganize-cluster.sh script
- Manual migration steps for edge cases
- Benefits of the new organization approach
- Critical registry update requirements

Includes examples for both complex (uppmax) and simple (sanger)
cluster configurations to guide future reorganizations.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

- Fix update-pipeline-configs.yml to create files in conf/pipeline/
  instead of pipeline/ to match current directory structure
- Fix typo "succesfully" → "successfully" in fix-linting.yml
- Fix duplicate step names in fix-linting.yml for better clarity
- Remove extra whitespace in conditional check

These fixes ensure automated pipeline config creation works correctly
with the reorganized directory structure.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Complete the mass migration of cluster configurations:

- Add mass migration automation script (migrate-all-clusters.sh)
- Migrate 134 clusters from conf/*.config to conf/*/nextflow.config
- Move pipeline-specific configs to organized subdirectories:
  - Move conf/pipeline/*/cluster.config → conf/cluster/pipelines/*/nextflow.config
  - Move docs/pipeline/*/cluster.md → conf/cluster/pipelines/*/README.md
- Update all registry paths in nfcore_custom.config automatically
- Remove all duplicate config and documentation files

This completes the infrastructure reorganization with:
- 137 total cluster directories (up from 3)
- All clusters now follow consistent structure pattern
- Co-located configuration and documentation
- Standardized naming (nextflow.config, README.md)
- 100% automated migration with zero manual fixes required

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>