Merge branch 'fix-shiva_fails' into 'develop'

Fix shiva fails

This branch will be used to fix found issues while running functional testing of shiva.

- [x] Fix report when not executing multisamplecalling
- [x] Fix missing key when no indelrealignment and base recalibration in summary
- [x] Fix wrong sample flag for single sample variant calling
- [x] Fix name of link when sample has only 1 lib
- [x] Added settings to Shiva summary
- [x] Raise default memory
- [x] Fix concordance checks

See merge request !261