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Point the workstation profile at /Volumes/ST5, the renamed Samsung T5 #46

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Merged
sr320 merged 1 commit into from
Oct 13, 2026
Merged

Point the workstation profile at /Volumes/ST5, the renamed Samsung T5 #46

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8 changes: 5 additions & 3 deletions config/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -62,8 +62,10 @@ profiles {
// docs/first_raw_reanalysis.md ("Storage layout"). Combine with an
// executor profile, e.g. `-profile local,workstation`.
//
// Samsung T5 (HFS+ SSD, ~450 MB/s) -> Nextflow work directory. Task
// folders are many small files and symlinks; keep them on the SSD.
// ST5, the Samsung T5 (HFS+ SSD, ~450 MB/s) -> Nextflow work directory.
// Task folders are many small files and symlinks; keep them on the
// SSD. The volume was renamed from "Samsung T5" on 2026-10-12: no
// path a tool sees may contain a space (see the docs page).
// blue-block (APFS HDD, ~140 MB/s, 4 TB) -> raw FASTQs and reference
// bundles, reached through the data/raw and data/reference symlinks.
//
Expand All @@ -76,7 +78,7 @@ profiles {
// Several study runs on one machine can share a work directory; Nextflow
// keys task folders by hash.
workstation {
workDir = System.getenv('AREE_WORKDIR') ?: '/Volumes/Samsung T5/aree/work'
workDir = System.getenv('AREE_WORKDIR') ?: '/Volumes/ST5/aree/work'
}
}

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17 changes: 16 additions & 1 deletion docs/first_raw_reanalysis.md
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Expand Up @@ -270,7 +270,7 @@ HFS+ or APFS, which support the symlinks and permissions Nextflow relies on.

| Location | Drive | Purpose |
|---|---|---|
| `/Volumes/Samsung T5/aree/work` | Samsung T5, SSD, ~450 MB/s | Nextflow work directory (`-profile workstation`) |
| `/Volumes/ST5/aree/work` | Samsung T5 (volume `ST5`), SSD, ~450 MB/s | Nextflow work directory (`-profile workstation`) |
| `/Volumes/blue-block/aree/raw/<STUDY_ID>/` | blue-block, HDD, 4 TB, ~140 MB/s | Raw FASTQs; `data/raw` is a symlink here |
| `/Volumes/blue-block/aree/reference/<ASSEMBLY>/` | blue-block | Transcriptome, GTF, tx2gene, Salmon index; `data/reference/<ASSEMBLY>` is a symlink here |
| `results/` | internal APFS | Published outputs, unchanged, so `aree harmonize` relative paths keep working |
Expand All @@ -287,6 +287,21 @@ The `workstation` profile lives in `config/base.config`, so every assay
workflow accepts it. Combine it with an executor profile
(`-profile local,workstation`); it sets only `workDir`.

**No path a tool sees may contain a space.** The SSD was mounted as
`/Volumes/Samsung T5` until 2026-10-12, which broke three things:
- Java split `NXF_TEMP` / `TMPDIR` on the space, so Nextflow failed before any
task started.
- Trim Galore and Bismark (Perl) pass the working directory unquoted to the
shell, and resolve it to its physical path. So they failed even through a
space-free symlink (`sh: /Volumes/Samsung: Operation not permitted`).
- Renaming the volume mid-run moved the publish directory out from under a
running job.

Renaming the volume to `ST5` fixes the first two. Don't give a data volume a
name with a space, and don't rename one while a run is publishing to it.
Workflow manifests written before the rename still record
`/Volumes/Samsung T5/...` as their `outdir`, which is where those runs wrote.

### Environment notes

* **Quarto fails on exFAT.** `RENDER_REPORT` dies in Quarto's cleanup
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