--outfile to msconvert.exe ignores the folder and outputs the file in the same folder as input

[hguturu]

Thermo-FAIMS-to-MzML/ThermoFAIMStoMzMLProcessor.cs

Line 212 in df2cb78

" --outfile {1}" +

It looks like the way the argument is processed by msconvert.exe causes the output files to be made in the same folder as the input files since it looks like outfile only override the default name, not the directory - https://proteowizard.sourceforge.io/tools/msconvert.html.

I think this will be fixed if this argument was split into

--outdir <- outputFile.DirectoryName
--outfile <- outputFile.Name