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bokulich-lab / q2-assembly

QIIME 2 plugin for (meta)genome assembly.
BSD 3-Clause "New" or "Revised" License
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ENH: read mapping to contigs using Bowtie2 #15

Closed misialq closed 2 years ago

misialq commented 3 years ago

Adds mapping NGS reads to contigs with Bowtie2 (via map-reads-to-contigs action).

Requires types defined in https://github.com/bokulich-lab/q2-types-genomics/pull/27

Closes #5.

codecov[bot] commented 2 years ago

Codecov Report

Merging #15 (dbb1f96) into main (f294746) will increase coverage by 0.31%. The diff coverage is 97.63%.

@@            Coverage Diff             @@
##             main      #15      +/-   ##
==========================================
+ Coverage   96.62%   96.94%   +0.31%     
==========================================
  Files           7       10       +3     
  Lines         356      458     +102     
  Branches       60       81      +21     
==========================================
+ Hits          344      444     +100     
- Misses          7        8       +1     
- Partials        5        6       +1
Impacted Files Coverage Δ
q2_assembly/_utils.py 95.74% <88.88%> (+0.62%) :arrow_up:
q2_assembly/bowtie2/utils.py 95.91% <95.91%> (ø)
q2_assembly/_action_params.py 100.00% <100.00%> (ø)
q2_assembly/bowtie2/indexing.py 100.00% <100.00%> (ø)
q2_assembly/bowtie2/mapping.py 100.00% <100.00%> (ø)
q2_assembly/plugin_setup.py 100.00% <100.00%> (ø)

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misialq commented 2 years ago

Thanks for review @ebolyen! I changed a bit the bowtie2's mode/sensitivity to follow what @nbokulich suggested. Merging when all checks ✅.

thermokarst commented 2 years ago

@misialq, just to close the loop on what library does with your packages once the github workflow (with action-library-packaging in it) here has run:

https://github.com/qiime2/package-integration/pull/237

that pr triggers workflows in that repo to attempt to "integrate" the package - basically just make sure it can be installed with everyone else in the community distro. if its ci is successful, library will auto-merge that pr.

after that, there are some cron workflows running on that repo - they take the integrated set of packages and then re-runs all of the individual package unit tests, to make sure that the resolved dependencies don't subtly break anything.