Fixed tophat unittests

This should fix failing unit tests for tophat

See merge request !220

Fix aligners

Some aligner are failing in testing, this should fix those issues

See merge request !217

Adding index file as output file for queue

Small fix to add the index file as output file for queue

See merge request !219

Feature improve sample tsv

Easy fox for #190 

See merge request !214

Feature fast build

Parallel data providers din't work very well. Adding `<forkCount>1C</forkCount>` do improve testing.

See merge request !213

(cherry picked from commit fb2fc695)

Skipping parts of report when they are skipped in the pipeline

Report of mapping fail when skip_flexiprep or skip_metrics is enabled, this should fix it.

See merge request !216

(cherry picked from commit 73990f01)

Added a better error handling on a missing reference.

Small change to better track missing references

See merge request !210

Issue186

See #186. 

See merge request !209

Changed dependency



See merge request !208

Ended up using HTSJDK nomenclature for genotype types
I.e: HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE