Metadata Table access for WES/WGS

[vinjana]

In contrast to WGBS, the WES and WGS workflows currently still use the extraction of execution parameters (sample, pid, etc.) from paths.

• Centralize all path parsing code (maybe in a service)
• Can the service be made a ParameterAccumulator that collects the data incrementally?
• Can the execution model be changed to first read all parameters (e.g. from the paths or the metadata table) and afterwards execute?

Furthermore,

• accept BAM file path as input and merge into existing BAM (inkremental merging)
• check that all read groups in the BAM are also provided in the metadata table (+ possibility to turn off this check)
• if all fastqs are already in the BAM do (1) nothing?, (2) mark again?, (3) only QC? -- best provide all three options as configurable behaviour.

Note that path-parsing code is also in RoddyCore. E.g. de.dkfz.roddy.core.RuntimeService#extractDataSetIDFromPath
It may be a possible to start in the AQCWF, generalize into COWF and even later in the RoddyCore, as was done for the MetadataTable. Then MetadataTable and PathExtraction may become strategies (Strategy Pattern). Others may be e.g. getting data from a database (such as OTP).