ENH: add action to estimate MAG abundance

[misialq]

This PR adds an action to estimate abundances of dereplicated MAGs in the original samples. The estimation is done in the following way:

1. Reads are mapped to the dereplicated MAGs (using the map-reads action from q2-assembly).
2. Coverage of each MAG is calculated using the samtools coverage command.
3. The metric of choice (RPKM or TPM) is calculated using the coverage report (from which the read counts per MAG are obtained) and reported in the final table.

Depends on bokulich-lab/q2-assembly#81.

[misialq]

/q2ci

Edit: Running QIIME 2 CI...

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.96%. Comparing base (e16ac9d) to head (bdeec3f).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #177      +/-   ##
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- Coverage   98.47%   97.96%   -0.52%     
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  Files          82      155      +73     
  Lines        4600     9298    +4698     
  Branches        0      409     +409     
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+ Hits         4530     9109    +4579     
- Misses         70      140      +70     
- Partials        0       49      +49     

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[github-actions]

This PR/issue depends on:

• ENH: add more indexing and read mapping options q2-assembly#81

[misialq]

For reviewers: this action was already tested against some real data so (unless you want to try it out) feel free to focus mostly on the code review. Thanks! 🙏

[ChristosMatzoros]

Hey @misialq, the code looks good to me! You can merge! 🚀