Make modules more flexible

[jpfeuffer]

Description of feature

I am not sure but I think in some modules we could reduce the hardcoding of parameters in the script and pass them with "withName" "ext.args" configs. In general, modules should only specify in- and output files and maybe the parameters from the channel. For OpenMS modules it is actually not so urgent, since you can specify a parameter twice and the last value will be taken. But other tools might fail if we don't do that. At least EVERY module should have an {args} at the end of the script to allow modification by developers and users.