JOSS review comments -- redux

[lincoln-harris]

this PR to address JOSS review comments from @betteridiot and @afrubin

• preface OS dependencies before install instructions

• remove -e from pip install instructions in README.md

• perhaps specify as pip install [--user] in README.md

• USAGE.md hyperlink in README.md is pointing to the wrong place?

• better explanation for report_coverage option, and perhaps specify that this is a boolean

• address this stdout message were seeing in report_coverage:

<class 'hgvs.edit.AASub'> <class>

• find-peptide-variants outfile is not in proper JSON format

• CONTRIBUTING.md hlink points the wrong place in USAGE.md

• tumor vs. normal phrasing in germline-filter section of paper.md
  (addressing this comment)

• update cmdline option names in germline-filter module to reflect tumor vs. normal phrasing

• updated Maynard, 2020 ref

• README: moved windows limitations to start of Installation section to address this comment

• README: made a note about WSL in Installation section to address this comment

• README: made a note that docker is the preferred installation method to address this comment

• README: add a 'for developers' subsection in Installation instructions

• README: add a 'Dependencies' subsection in Installation instructions

• README: made a note that PyPi install is NOT recommended

• added Topic :: Scientific/Engineering :: Bio-Informatics classifier

• add issue reporting template (possibly in CONTRIBUTING.md)

• replace report_coverage option with click boolean flag in find-peptide-variants

[codecov]

Codecov Report

Merging #109 into master will decrease coverage by 0.12%.
The diff coverage is 93.33%.

@@            Coverage Diff             @@
##           master     #109      +/-   ##
==========================================
- Coverage   93.08%   92.95%   -0.13%     
==========================================
  Files           8        8              
  Lines         723      724       +1     
==========================================
  Hits          673      673              
- Misses         50       51       +1     

Impacted Files	Coverage Δ
cerebra/utils.py	88.33% <ø> (-0.05%)	⬇️
cerebra/find_peptide_variants.py	98.63% <75.00%> (-0.68%)	⬇️
cerebra/count_variants.py	96.77% <100.00%> (ø)
cerebra/germline_filter.py	96.77% <100.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update df33e2f...451e1bd. Read the comment docs.