stitch-cosmx.jl is not working

[roanvanscheppingen]

Not familiar with julia, but it's not working. Using julia stitch-cosmx_RVS2.jl ../../rp_5/image_data/cosm03_images/MsBrainTMA/20240229_204141_S1/ transcripts.csv.gz

ERROR: LoadError: BoundsError: attempt to access 0-element Vector{String} at index [1]
Stacktrace:
 [1] getindex
   @ ./essentials.jl:13 [inlined]
 [2] main()
   @ Main /hpc/shared/prekovic/rvanscheppingen/Julia/stitch-cosmx_RVS2.jl:31
 [3] top-level scope
   @ /hpc/shared/prekovic/rvanscheppingen/Julia/stitch-cosmx_RVS2.jl:105

I think it has to do with calling the directory. Currently the code has config_filename = glob("S0/*/RunSummary/*_ExptConfig.txt", path)[1]

However, there is no S0 folder in the path. The path is image_data/cosm03_images/MsBrainTMA/20240229_204141_S1

Subdirectories are the RunSummary etc, as they should be. AnalysisResults AnalysisResultsArchived CellStatsDir plex-usm2wp948s.txt RunSummary

Running nano on the txt works and opens the file. nano MsBrainTMA/20240229_204141_S1/RunSummary/*_ExptConfig.txt

Note that in my edit of the .jl I've changed S0//RunSummary to ./RunSummary, but I have also tried .//RunSummary. Something similar was raised in #3 , but the fix implemented after kept the S0

Thanks in advance!