Conversion from input path containing wildcard (rather than file path) to dir doesn't work for me

[m-albert]

Thanks a lot for this great tool! Installation worked like a charm, as well as conversion for individual files.

However when I try to use a command like:

batchconvert omezarr /path/to/input/dir/*.czi /path/to/output/dir

to use a wildcard to indicate the files I want to convert, with a directory as a destination path, I get error messages as the following:

[7b/fbcfd9] NOTE: Missing output file(s) `Example file.ome.zarr` expected by process `Convert2OMEZARR_FromLocal:Convert_EachFileFromRoot2SeparateOMEZARR (9)` -- Execution is retried (1)

Yes, my files have spaces in their paths 🙈

Thanks!

[bugraoezdemir]

Hi @m-albert ,
Sorry for being late. Can you try with the input path with wildcard in quotes like this:
batchconvert omezarr "/path/to/input/dir/*.czi" /path/to/output/dir
Let me know if that helps.