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Integration of BUSCO as a qiime2 visualizer in q2_moshpit #60

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merged 92 commits into from
Oct 9, 2023

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Sann5
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@Sann5 Sann5 commented Sep 5, 2023

  • Makes BUSCO available as a qiime2 visualizer.
  • Tests the implementation.

TODO:

  • Update the tutorial in the wiki such that it shows an example of the use of BUSCO.

Closes #57

@misialq
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misialq commented Oct 5, 2023

Hey @Sann5, also here, could you please rebase/merge the main branch? You'll also need to resolve some conflicts, while at that 😬

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codecov bot commented Oct 6, 2023

Codecov Report

Merging #60 (548529a) into main (2b11966) will increase coverage by 0.01%.
The diff coverage is 97.70%.

@@            Coverage Diff             @@
##             main      #60      +/-   ##
==========================================
+ Coverage   97.56%   97.58%   +0.01%     
==========================================
  Files          27       32       +5     
  Lines        1645     1945     +300     
==========================================
+ Hits         1605     1898     +293     
- Misses         40       47       +7     
Files Coverage Δ
q2_moshpit/__init__.py 100.00% <100.00%> (ø)
q2_moshpit/busco/__init__.py 100.00% <100.00%> (ø)
q2_moshpit/busco/busco.py 100.00% <100.00%> (ø)
q2_moshpit/busco/tests/test_busco.py 100.00% <100.00%> (ø)
q2_moshpit/busco/utils.py 100.00% <100.00%> (ø)
q2_moshpit/plugin_setup.py 100.00% <100.00%> (ø)
q2_moshpit/tests/test_utils.py 96.00% <100.00%> (+0.87%) ⬆️
q2_moshpit/_utils.py 90.47% <50.00%> (-4.77%) ⬇️
q2_moshpit/busco/tests/test_utils.py 95.31% <95.31%> (ø)

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@Sann5 Sann5 merged commit 70afdfa into bokulich-lab:main Oct 9, 2023
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@Sann5 Sann5 deleted the busco branch October 9, 2023 12:58
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implement MAG evaluation using BUSCO
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