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refactor(workflow): guard the stage store with a touch() sentinel #29

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Merged
lguerard merged 1 commit into from
Jun 24, 2026
Merged

refactor(workflow): guard the stage store with a touch() sentinel #29

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4 changes: 4 additions & 0 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@ IMAGE = f"{WORK}/image.zarr"
IMAGE_OK = f"{IMAGE}/zarr.json"
TILES = f"{WORK}/tiles.json"
STAGE = f"{WORK}/stage.zarr"
# Completion sentinel for the stage store. Tracking a touch()ed marker instead
# of directory(STAGE) keeps Snakemake from deleting/recreating the store on a
# re-run and avoids directory-mtime quirks (same touch() discipline as sopa).
STAGE_OK = f"{STAGE}.done"


def occupied_done(wildcards):
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4 changes: 2 additions & 2 deletions workflow/rules/segment.smk
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Expand Up @@ -5,7 +5,7 @@ checkpoint prepare:
IMAGE_OK,
output:
tiles=TILES,
stage=directory(STAGE),
stage=touch(STAGE_OK),
script:
"../scripts/prepare_tiles.py"

Expand All @@ -14,7 +14,7 @@ rule segment:
"""Segment one tile on a GPU and write it into the stage store."""
input:
tiles=TILES,
stage=STAGE,
stage=STAGE_OK,
image=IMAGE_OK,
output:
f"{WORK}/seg/{{index}}.done",
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