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clemente-lab / mmeds-meta

A database for storing and analyzing omics data
https://mmeds.org
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Enhancement adding analysis tools #425

Closed adamcantor22 closed 1 year ago

adamcantor22 commented 1 year ago

Pull Request Template for MMEDS

What has changed

Four new analysis tools have been added: CUTIE, SparCC, PiCRUSt2, and LeFSe. There has also been various improvements to analyses in general, allowing for files to be used between different tools, more specific config files, and being able to run analyses from the command line. Code coverage is also significantly improved, with analysis tools being reintroduced in the testing framework.

Checklist of pre-requisites

How to use the feature

To run an analysis manually use the run_analysis.py script in a mmeds environment. View this script's --help for details. Alternatively, these tools are available as normal in the web UI. web01 is only partially up though, so the jobs need to be manually submitted on another node once they're created until it's fully back up.

Issue closings

Closes #229 Closes #355 Closes #354 Closes #361

codecov[bot] commented 1 year ago

Codecov Report

Base: 58.07% // Head: 73.92% // Increases project coverage by +15.85% :tada:

Coverage data is based on head (64e5e47) compared to base (c2796ee). Patch coverage: 80.18% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #425 +/- ## =========================================== + Coverage 58.07% 73.92% +15.85% =========================================== Files 30 32 +2 Lines 5421 5664 +243 =========================================== + Hits 3148 4187 +1039 + Misses 2273 1477 -796 ``` | Flag | Coverage Δ | | |---|---|---| | server | `46.64% <17.61%> (-2.23%)` | :arrow_down: | | unit | `?` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab) | Coverage Δ | | |---|---|---| | [mmeds/database/database.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvZGF0YWJhc2UvZGF0YWJhc2UucHk=) | `69.17% <0.00%> (+22.04%)` | :arrow_up: | | [mmeds/database/documents.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvZGF0YWJhc2UvZG9jdW1lbnRzLnB5) | `84.34% <ø> (+31.30%)` | :arrow_up: | | [mmeds/util.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdXRpbC5weQ==) | `68.59% <36.48%> (+14.99%)` | :arrow_up: | | [mmeds/spawn.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvc3Bhd24ucHk=) | `65.78% <40.00%> (+1.66%)` | :arrow_up: | | [mmeds/server.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvc2VydmVyLnB5) | `70.00% <60.00%> (+0.20%)` | :arrow_up: | | [mmeds/tools/tool.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdG9vbHMvdG9vbC5weQ==) | `60.40% <90.76%> (+47.44%)` | :arrow_up: | | [mmeds/tools/lefse.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdG9vbHMvbGVmc2UucHk=) | `95.23% <96.00%> (+76.71%)` | :arrow_up: | | [mmeds/tools/cutie.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdG9vbHMvY3V0aWUucHk=) | `96.87% <96.87%> (ø)` | | | [mmeds/tools/picrust2.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdG9vbHMvcGljcnVzdDIucHk=) | `96.96% <96.96%> (ø)` | | | [mmeds/tools/sparcc.py](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab#diff-bW1lZHMvdG9vbHMvc3BhcmNjLnB5) | `98.50% <97.29%> (+80.72%)` | :arrow_up: | | ... and [20 more](https://codecov.io/gh/clemente-lab/mmeds-meta/pull/425/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=clemente-lab)

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