AGENTS.local.md.example

# Local Agent Notes

This file is intentionally a local, untracked override for host-specific paths
and installation details.

Usage:
- Copy this file to `AGENTS.local.md`
- Edit the copied file for the local machine
- Do not commit `AGENTS.local.md`

Suggested contents:

## Canonical Local References

- Local harmonized GRCh38 STAR index:
  `/storage/autoindex_110_44/bulk_index`
- Cell Ranger-style wrapper around the same local index:
  `/storage/autoindex_110_44/refdata-gex-GRCh38-autoindex11044-cellranger`

## Important Reference Provenance

- `/storage/autoindex_110_44/refdata-gex-GRCh38-autoindex11044-crstar/star`
  is not a local STAR build. Its `star/` files resolve into:
  `/storage/A375-CR-9.01/refdata-gex-GRCh38-2024-A/star`
- Use it only when you explicitly want the Cell Ranger frozen STAR index.

## Local Policy

- For STAR-only analysis, prefer:
  `/storage/autoindex_110_44/bulk_index`
- For Cell Ranger-style wrappers that should still use the local STAR index,
  prefer:
  `/storage/autoindex_110_44/refdata-gex-GRCh38-autoindex11044-cellranger`
- Do not assume similarly named GRCh38 reference roots use distinct STAR
  indices. Check symlink targets first.