QC under one umbrella (well mostly) under QuaC

QuaC is heavily reworked to be a companion pipeline to small variant caller pipeline and will now perform most of the QC analyses for WGS/WES data.

• While the small caller pipeline will still run few QC tools (for pragmatic reasons), QuaC will now take over the heavylifting of QC, including the QC-checkup.
• QuaC can perform both sample-level and project-level QC. This is the major reason why it was decided to separate QC from small-variant caller pipeline, as it could only perform single-sample QC.
• More QC tools were added
• For QC checkup, QuaC now heavily expands to vcf metrics and adds significant amount of QC thresholds for bam metrics.
• QuaC's input are output from the small variant caller pipeline, and former's output will fit seemlessly with the latter's output.
• QuaC accepts pedigree file as input. A dummy pedigree file creator script is provided, which will be handy until phenotips is made available to us.
• System-level testing is added

Following may need to be included as part of the MR review:

• Documentation review
• Install QuaC and run it with test dataset
• Review thresholds and metrics defined in QC-checkup config file
• Is testing performed sufficient?
• Is the repo reasonably structured?
• Review MR template

Note to self: Ensure following are discussed or taken care of before merging:

• Include workflow config file as part of repo or not (#20 (closed))
• Remove panoptes before merging the branch to master (#23 (closed))
• Need alternative name for "CGDS QC checkup"? (#24 (closed))
• Set --rerun_failed to 1 before merging [#22 (closed)]
• Mean and median coverage stats vary heavily between Qualimap and Picard. Which one to use? (#16 (closed))
• Update changelog.md