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Add the roadmap to the docs
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Roadmap | ||
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This document describes our future plans for additions to PopPUNK, `pp-sketchlib <https://github.com/bacpop/pp-sketchlib>`__ and `BeeBOP <https://github.com/bacpop/beebop/>`__ | ||
and BeeBOP. Tasks are in order of priority. | ||
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PopPUNK | ||
------- | ||
1. Containerise the workflow. See `#193 <https://github.com/bacpop/PopPUNK/issues/193>`__, `#277 <https://github.com/bacpop/PopPUNK/issues/277>`__, `#278 <https://github.com/bacpop/PopPUNK/issues/278>`__. | ||
2. Add full worked tutorials back to the documentation `#275 <https://github.com/bacpop/PopPUNK/issues/275>`__. | ||
3. Make the update pipeline more robust. See `#273 <https://github.com/bacpop/PopPUNK/issues/273>`__. | ||
4. Codebase optimsation and refactoring | ||
- Modularisation of the network code `#249 <https://github.com/bacpop/PopPUNK/issues/249>`__. | ||
- Removing old functions `#103 <https://github.com/bacpop/PopPUNK/issues/103>`__ | ||
5. Add more species databases: | ||
- N. meningitidis `#267 <https://github.com/bacpop/PopPUNK/issues/267>`__. | ||
- H. influenzae `#276 <https://github.com/bacpop/PopPUNK/issues/276>`__. | ||
6. Stable names for lineage/subclustering modes. | ||
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Other enhancements listed on the `issue page <https://github.com/bacpop/pp-sketchlib/issues>`__ are currently not planned. | ||
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pp-sketchlib | ||
------------ | ||
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1. Update installation in package managers | ||
- Update for new macOS `#92 <https://github.com/bacpop/ska.rust#planned-features>`__ | ||
- Rebuild conda recipe for CUDA12 and newer HDF5 `#46 <https://github.com/conda-forge/pp-sketchlib-feedstock/pull/46>`__ | ||
2. Allow amino-acids as input `#89 <https://github.com/bacpop/pp-sketchlib/issues/89>`__. | ||
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Other enhancements listed on the `issue page <https://github.com/bacpop/pp-sketchlib/issues>`__ are currently not planned. | ||
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BeeBOP | ||
------ | ||
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1. Update backend database to v8 `#42 <https://github.com/bacpop/beebop/pull/42>`__. | ||
2. Update CI images. | ||
3. Add more info on landing page. | ||
- News page. | ||
- About page. | ||
- Methods description. | ||
4. Add custom cluster names (e.g. GPSCs) | ||
5. Integration tests for error logging. | ||
6. Persist user data. | ||
- Persist microreact tokens `#41 <https://github.com/bacpop/beebop/pull/41>`__. | ||
- Allow user to change or delete tokens | ||
7. Add linage/subclusters to results page `#23 <https://github.com/bacpop/beebop/pull/23>`__. | ||
8. Report sample quality to user. | ||
9. Front-end update for large numbers of input files. | ||
10. Add serotype prediction for *S. pneumoniae*. | ||
11. Add multiple species databases. |