metamorpheus and rescue+resolve

[rsalz]

I would like to use metamorpheus + rescue and resolve, so I'm having a look at main_metamorpheus.nf to try to run it.

Some questions:
1 - can't find the toml file that you use. Why do you only run 1 TOML when metamopheus recommends 5 TOML files?
2- why are you converting .raw with msconvert? Metamorpheus can take raw files as input.
3- I have an experimental design tsv that works with metamorpheus for normalization purposes, where does this fit in
4- generally how to run this nextflow file by itself, isn't clear by looking at the notes in the file

Thanks!