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Refactor the report generation a bit. Move pipeline specific report components into the pipeline itself (not hosted in core anymore)

Fix coverage piping

Fixes #230 

still need testing

See merge request !257

Added GenotypeConcordance

Fixes #227, #228 and #229 

Adding here GenotypeConcordance of gatk. This can calculate concordance on multisample vcf files.

See merge request !260

Fix shiva bcftools calling

- [x] Test bcftools
- [x] Add merge to bcftools singlesample
- [x] Test bcftools singlesample


See merge request !254

Fix sample names on VCFs used in by tool tests

 * Replaces identifiers (e.g. Child_something) with `Sample_101` etc. 
 * Some proper temp file creation for more tools 

See merge request !259