Option to skip mzml conversion

[sooheon]

mzml conversion takes up a significant portion of runtime, and dia-nn now supports using .raw directly: https://github.com/vdemichev/DiaNN?tab=readme-ov-file#raw-data-formats

[ypriverol]

Thanks for the issue @sooheon we will work on it for the next release, however, some of the downsides of not converting are related with:

• pmultiqc will not work because we don't have easy access to RAW data from Python.
• Other components in the pipeline that use mzML will not work.

But agree, if the main idea is to speed-up DIANN, then we should make sure that we can read natively RAW files.