fix(workflow): skip OME-ZARR conversion when the store already exists - #26
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Make the convert rule's output a marker file inside the store (image.zarr/zarr.json) instead of directory(IMAGE), mirroring the sopa ".zgroup trick". Snakemake then natively skips conversion when the store already exists and never wipes the whole store on a re-run, so an expensive convert is not redone. Downstream rules depend on the marker. Drops the earlier overwrite_zarr config flag / in-script existence guard in favour of plain Snakemake DAG semantics. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Re-running the workflow no longer redoes the (expensive) OME-ZARR conversion if
image.zarralready exists.Adopts the idiomatic Snakemake approach used by imcf/sopa: the
convertrule'soutput:is a single marker file inside the store (image.zarr/zarr.json) instead ofdirectory(IMAGE). Snakemake then:convertwhen the marker exists (no custom guard / config flag), anddirectory()pre-delete hazard).Downstream rules depend on the marker file. Removed the earlier
overwrite_zarrflag and in-script existence check.To force a fresh conversion: delete
image.zarrorsnakemake --forcerun convert.Test
End-to-end on a synthetic CZYX OME-TIFF (
thresholdmethod, no GPU):image.zarr): job stats list onlyprepare+segment+merge—convertabsent, store reused. 11/11 done.🤖 Generated with Claude Code