ENH: co-assembling contigs from multiple samples (#22)

[DorielaGrabocka]

This draft PR contains code for co-assembly in MEGAHIT

Depends on: qiime2/q2-types#314.

[misialq]

Hey @DorielaGrabocka, here are a few code suggestions :) Also, you should look at the CI and see which tests are failing - those may need some adjustments (obv, you can also do it locally). Plus introducing a new test for testing the co-assembly :)

[codecov]

Codecov Report

Attention: Patch coverage is 96.64804% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 98.28%. Comparing base (debd89a) to head (71dd4eb).
Report is 4 commits behind head on main.

Files	Patch %	Lines
q2_assembly/megahit/megahit.py	76.47%	4 Missing ⚠️
q2_assembly/_utils.py	92.85%	1 Missing ⚠️
q2_assembly/spades/tests/test_spades.py	97.56%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #68      +/-   ##
==========================================
- Coverage   98.54%   98.28%   -0.26%     
==========================================
  Files          25       27       +2     
  Lines        1443     1752     +309     
==========================================
+ Hits         1422     1722     +300     
- Misses         21       30       +9     

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[misialq]

Hey @DorielaGrabocka, see some comments below - I'm still trying the code out on some samples ;)

[misialq]

Great, thanks @DorielaGrabocka! 🏅