refactoring how external scripts and locations are called

[zktuong]

Main thing is to refactoring code to call external scripts and locations more cleanly

• Convert to using pathlib for everything when it requires to access files
• Refactor create_germlines to just call CreateGermlines.py directly
• • Define clones within each group #279
• • Accept metadata column as clones for germline inference (pp.create_germlines) #281
• • Add outfile_dir to define_clones #282
• Try and check for spellings, and remove unnecessary arguments.
• Remove deprecated functions

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[codecov]

Codecov Report

Merging #288 (5d3b9cf) into master (464c4a3) will increase coverage by 0.56%.
The diff coverage is 90.80%.

@@            Coverage Diff             @@
##           master     #288      +/-   ##
==========================================
+ Coverage   82.21%   82.78%   +0.56%     
==========================================
  Files          47       47              
  Lines        9065     8514     -551     
==========================================
- Hits         7453     7048     -405     
+ Misses       1612     1466     -146     

Flag	Coverage Δ
unittests	82.78% <90.80%> (+0.56%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dandelion/__init__.py	100.00% <ø> (ø)
dandelion/logging/__init__.py	100.00% <ø> (ø)
dandelion/logging/_badge.py	100.00% <ø> (ø)
dandelion/logging/_logging.py	100.00% <ø> (ø)
dandelion/logging/_metadata.py	77.77% <ø> (-2.23%)	⬇️
dandelion/plotting/__init__.py	100.00% <ø> (ø)
dandelion/plotting/_plotting.py	82.73% <ø> (-0.06%)	⬇️
dandelion/preprocessing/__init__.py	100.00% <ø> (ø)
dandelion/preprocessing/external/__init__.py	100.00% <ø> (ø)
dandelion/tools/__init__.py	100.00% <ø> (ø)
... and 35 more