Quentin Blampey

Weirdly enough, it seems that snakemake uses an incorrect path. Indeed, in your logs I see `tuto.zarr.sopa_cache\cellpose_boundaries\3.parquet`, but there is a missing `\`, since it should be `tuto.zarr\.sopa_cache\cellpose_boundaries\3.parquet` I don't...

Good to hear that the CLI works. I changed something in the way to handle the paths in the snakemake pipeline. Maybe it will fix this "missing `/`" issue, but...

I just released `sopa==1.1.0`, it should fix at least the encoding issue, can you check?

Hello @josenimo, Can you check if the "missing" files are really missing? E.g., does this file exist? ``` C:\Users\jnimoca\Desktop\SOPA\sopa\workflow\data\991_subset.ome.zarr\.sopa_cache\cellpose_boundaries\10.parquet ``` If the file exists, then snakemake is not detecting it...

Ok thanks for the details. I think it's an issue related to snakemake, which doesn't trigger the rules that create the input needed for the `resolve_cellpose` rule Can you tell...

Hello all, Sorry for taking so long, I couldn't find a Windows that I could take for a few hours/days to reproduce the issue. One solution to move forward could...

Hello all, I finally found out the issue, which is that snakemake, for some reason, doesn't handle Windows path when provided by pathlib. This is fixed and will be available...

Sorry for the delay! I’m happy to announce that `sopa==2.0.0` is now released :) It should fix this issue, please let me know if it doesn't

Thanks @jeffquinn-msk, I'll have a look!

Hello @suhridbuddha, the `tuto.zarr` directory should be located in the directory where you executed the pipeline, i.e. in the `workflow` directory. Was the pipeline successfully executed? Do you have the...