diff --git a/README.md b/README.md index 3ca13f15..f8bbc49a 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,9 @@ doi:[10.1101/gr.241455.118](https://doi.org/10.1101/gr.241455.118) You can also run your command with `--citation` to get a [list of citations](https://poppunk.readthedocs.io/en/latest/citing.html) and a suggested methods paragraph. -## News +## News and roadmap + +The [roadmap](https://poppunk.readthedocs.io/en/latest/roadmap.html) can be found in the documentation. ### 2023-01-18 diff --git a/docs/index.rst b/docs/index.rst index bd50f8c0..0dabfc6f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -48,6 +48,7 @@ in the `paper `_. poppunk_iterate.rst citing.rst api.rst + roadmap.rst miscellaneous.rst Why use PopPUNK? diff --git a/docs/roadmap.rst b/docs/roadmap.rst new file mode 100644 index 00000000..6f76b6a6 --- /dev/null +++ b/docs/roadmap.rst @@ -0,0 +1,53 @@ +Roadmap +==================================== + +.. |nbsp| unicode:: 0xA0 + :trim: + +This document describes our future plans for additions to PopPUNK, `pp-sketchlib `__ and `BeeBOP `__ +and BeeBOP. Tasks are in order of priority. + +PopPUNK +------- +1. Containerise the workflow. See `#193 `__, `#277 `__, `#278 `__. +2. Add full worked tutorials back to the documentation `#275 `__. +3. Make the update pipeline more robust. See `#273 `__. +4. Codebase optimsation and refactoring + - Modularisation of the network code `#249 `__. + - Removing old functions `#103 `__ +5. Add more species databases: + - N. meningitidis `#267 `__. + - H. influenzae `#276 `__. +6. Stable names for lineage/subclustering modes. + +Other enhancements listed on the `issue page `__ are currently not planned. + +pp-sketchlib +------------ + +1. Update installation in package managers + - Update for new macOS `#92 `__ + - Rebuild conda recipe for CUDA12 and newer HDF5 `#46 `__ +2. Allow amino-acids as input `#89 `__. + +Other enhancements listed on the `issue page `__ are currently not planned. + +BeeBOP +------ + +1. Update backend database to v8 `#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 `__. + - Allow user to change or delete tokens +7. Add linage/subclusters to results page `#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.