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

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

Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221

Fixes #221 

See merge request !258

Reorganize output json, including unclassified readcount

Update filename + extension retrieval in Flexiprep

Two changes:

* Refactored the uncompressed filename + extension retrieval. Also made sure now that extension trimming is case-insensitive (".gzip" and ".GZIP" are both trimmed).

* Added a clearer error message when the input file doesn't have any extension.

See merge request !256

Fixes #213

Quick fix for #213 

See merge request !249