CNV Tumor only WDL

[LeeTL1220]

Fixes #3983

• Added two tumor-only tests to the CNV WDL test. I did not add all four possible combinations, since I did not see the value. I just wanted to make sure that the WGS and WES cases were covered.

[samuelklee]

Just a couple of very minor comments. Thanks @LeeTL1220!

[samuelklee]

Remove white space to be consistent.

[LeeTL1220]

Done

[samuelklee]

Anything stopping you from putting all of the tasks for the normal in a single if block? (If so, no biggie.)

[LeeTL1220]

@samuelklee I just wanted to preserve the order. My logic was simply so that we keep the like tasks together. If you would like me to change it, no problem. Just tell me.

[samuelklee]

I think it's fine to put them all in the same block.

At some point, we can extract a single-sample subworkflow that takes allelic counts from a matched normal as an optional input to the ModelSegments task (since that is the only difference between running the normal and the tumor). This pair workflow will just be two calls to that single-sample workflow. However, this can definitely wait until Cromwell handles subworkflows more elegantly.

[LeeTL1220]

@samuelklee Put the normal sample processing into one if block.

[codecov-io]

Codecov Report

Merging #4414 into master will increase coverage by 0.002%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #4414       +/-   ##
===============================================
+ Coverage     79.024%   79.025%   +0.002%     
+ Complexity     16447     16446        -1     
===============================================
  Files           1047      1047               
  Lines          59186     59186               
  Branches        9672      9672               
===============================================
+ Hits           46771     46772        +1     
- Misses          8659      8660        +1     
+ Partials        3756      3754        -2

Impacted Files	Coverage Δ	Complexity Δ
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...park/sv/discovery/alignment/AlignmentInterval.java	90.038% <0%> (+0.766%)	74% <0%> (+1%)	⬆️
...e/hellbender/engine/spark/SparkContextFactory.java	73.973% <0%> (+2.74%)	11% <0%> (ø)	⬇️