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.