Leftover `.tif` files in the output folder

haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas

MIT License

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Leftover `.tif` files in the output folder #137

Closed prete closed 3 months ago

prete commented 3 months ago

After running the pipeline (_input data 10x Xenium with analysis_sw_version: xenium-3.0.0.15_) I get anndata.zarr, label.zarr,raw.zarr and config.json. But there is also a label.tif file being created in the output folder that shouldn't be there.

The file seems to be generated here in process_xenium.py and it's probably published by the Generate_image process.

Should that be part of the output?

dannda commented 3 months ago

Agree that shouldn't be in the output by default

prete commented 3 months ago

Fixed #138