Remove EXTRACTPSMFEATURES/IDScoreswitcher from workflow

[ypriverol]

Description of feature

In the latest OpenMS (dev) version, the FeatureExtraction process happens within each Search engine adapter MSGFAdapter, SAGEAdapter, etc. We don't have to rerun this step for every Search engine, then this step can be removed it.

Thoughts @timosachsenberg @jpfeuffer before starting.

[jpfeuffer]

Also remove IDScoreswitcher. I think @timosachsenberg merged my simplification changes

[timosachsenberg]

I defnitely merged also some IDScoreSwitcher changes but I did not test it in the context of quantMS. I think it is a valuable change but should be done with two PRs that are each tested on some small data.

[ypriverol]

What about changing all the tests in singularity and docker to point to OpenMS Dev. Which we sync the test and new deployments and changes in OpenMS with quantms more clearly-tidy. ?

[ypriverol]

Related to this topic, we have one flag called posterior_probabilities = 'percolator' this flag defines the posterior_probabilites used in the workflow. However, I have never run this flag without that value. Can we remove it @daichengxin @jpfeuffer? We should always use Percolator probabilities.

[daichengxin]

We could remove this parameter and the corresponding modules if we make sure always use the Percolator probability. But I don't see any harm in leaving it there. I don't know if any other users use it, at least we

[ypriverol]

No harm, but confusing if is always used with same value.

[jpfeuffer]

Fine with me. Percolator will not work for very small data though.

[ypriverol]

How small are we talking here?

[jpfeuffer]

Hard to say. @timosachsenberg knows better.
1000 PSMs after FDR filter?

[ypriverol]

Ok, quantms is not designed for that anyway. I haven't seen any msruns with less that 1k psms.

[timosachsenberg]

Hard to say. @timosachsenberg knows better. 1000 PSMs after FDR filter?

Yeah maybe 400 would still work.
I think we added it as fallback to be able to analyze small studies or blanks (!) if we do per file percolator

[ypriverol]

If people don't use it really, it should be here unless someone needs it, BTW, the pipeline becomes more complex for something that hardly happens.

BTW, @timosachsenberg @jpfeuffer @daichengxin The PR removing posterior_probabilities = 'percolator' is ready here #450