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Deprecate conda, make pipeline more general

Merged van den Berg requested to merge known-snps into master
  1. Deprecate conda in favour of singularity
  2. Convert all test cases to use conda
  3. Fix a bug in the coverage calculation that was caused by singularity
  4. Remove the external gatk.jar file as a dependency
  5. Specify 1 or more vcf files for base recalibration, instead of ONETHOUSAND, HAPMAP, ONETHOUSAND
Edited by van den Berg