Point the workstation profile at /Volumes/ST5, the renamed Samsung T5

[sr320]

What and why

The Samsung T5 SSD that holds the Nextflow work directory was renamed from Samsung T5 to ST5 on 2026-10-12, so it now mounts at /Volumes/ST5. -profile workstation still pointed at /Volumes/Samsung T5/aree/work, which no longer exists. Any run using the profile without AREE_WORKDIR set would fail.

• config/base.config: the workstation profile's default workDir is now /Volumes/ST5/aree/work, and the comment explains the rename.
• docs/first_raw_reanalysis.md ("Storage layout"):
  • the table row is updated;
  • a new note says no path a tool sees may contain a space, and lists what the space broke: Java splitting NXF_TEMP, and Trim Galore / Bismark resolving the physical working directory so that even a space-free symlink failed;
  • it warns against renaming a volume while a run is publishing to it.
• Not changed: the committed workflow manifests for IOCAS2022 and LUTIER2022 still record /Volumes/Samsung T5/... as their outdir. That's where those runs actually wrote, so the provenance stays as is.

Checklist

• pytest -q and ruff check src tests pass (467 passed; no Python changes)
• New logic has a test. Not applicable: config path and docs only. nextflow config workflows/rnaseq -profile local,workstation resolves workDir = '/Volumes/ST5/aree/work', and that folder exists.
• Relevant docs/ page updated
• Study branches that need this change are listed below, so they can rebase after it merges

Study branches waiting on this

None. The running CIBNOR job (#14) sets its own work dir on blue-block and already publishes to /Volumes/ST5.

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