Finish CM implementation

[apeltzer]

Missing parts:

Handling SE data
FixPrefix for AR - when to combine which files?
merging vs only clipping for both

[apeltzer]

The pipelin should be able to handle these kind of datasets:

• Single Ended
• Paired Ended

In both cases, we'd like to see adapters to be removed. Additionally for PE data, there needs to be read merging performed with several output files that are then combined to a single file for downstream analysis.

An example on what is done normally can be found here:

https://github.com/apeltzer/EAGER-CLI/blob/master/src/main/java/Modules/preprocessing/CombineFastQ.java

I personally think we should also get rid of Clip&Merge and just support AdapterRemoval in EAGER2, no need for having two methods when one is anyways outperforming the other in all cases.

[apeltzer]

Dropping CM implementation for AdapterRemovalv2 implementation. That should suffice for 99.5% of all projects anyways.