M2 NIO wdl -- updated for Firecloud pet service accounts

[davidbenjamin]

@LeeTL1220 Ready for review. I will concurrently test in Firecloud.

[LeeTL1220]

Looks okay. I made a comment, but it does not necessarily require action.

I compared this to the non-NIO version of the M2 WDL (in this branch/master) for my review.

[LeeTL1220]

Why eliminate all the index files? Seems like that will make it harder to keep the files in sync. Your call.

[LeeTL1220]

If it works in FC, then feel free to merge. Addressing my comment is your decision.

[codecov-io]

Codecov Report

Merging #4710 into master will increase coverage by 0.006%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##             master     #4710       +/-   ##
==============================================
+ Coverage     79.85%   79.856%   +0.006%     
- Complexity    17339     17341        +2     
==============================================
  Files          1074      1074               
  Lines         62932     62932               
  Branches      10183     10183               
==============================================
+ Hits          50251     50255        +4     
+ Misses         8703      8699        -4     
  Partials       3978      3978

Impacted Files	Coverage Δ	Complexity Δ
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+40%)	3% <0%> (+2%)	⬆️

[davidbenjamin]

Working on Firecloud after one tweak: if [ -f ${normal_bam} ] doesn't work when normal_bam is a String because nothing is localized, so I replaced it with if [ ! -z ${normal_bam} ]. I will merge around 6 am after Travis tests hopefully pass.