Specifying the output directory

[yonist]

I'm running MSFragger from the command line as part of a pipeline. I need away to control the output directory (I found only a parameter to control the output format but not the location where the file will be created) is there one? if not what are the rules for the location (it seems to behave differently if it runs in local docker vs ECS)

Thanks,

p.s.
If this is not the right place to ask these kind of questions please direct me to it.

[fcyu]

MSFragger writes the output to the folder where the mzML/raw/mgf files are in.

Best,

Fengchao

[yonist]

Thanks. If you can add this feature that would be great.

As a side note I have an edge case, which doesn't work as you said, I'm running MSFragger in a docker and the results are written in the /app directory and not on the external mounted volume which contains the mzBIN file.

[fcyu]

Hmm, I never tested MSFragger in docker. Thanks for the bug report. I will take a look and maybe add parameter to specify the output location. We had one before but haven't used it for a long time.

Best,

Fengchao

[yonist]

If you cannot reproduce it contact me and we can do a zoom/meet.