Major Changes
1. This release is a complete overhaul of the inner workings of readfish. Fundamentally nothing has changed in the way readfish works, but we have dramatically improved the compatibility with nanopore platforms, as well as supporting more compute systems including Apple Silicon.
2. This release is compatible with all flavours of PromethION from the lonely p2solo to the gregarious P48. To do this we include a new rust based wrapper for minimap2 which enables multi-threaded mapping. The release also supports GridION and MinION. It is untested on mk1c and we don't recommend using it.
3. This release is compatible with both guppy and dorado via the `ont-pyguppy-client-lib` and so introduces native support for apple silicon.
4. We also introduce a new readfish stats module which will summarise an experiment given the TOML configuration for readfish and the path to the FASTQs from the run.
5. The code includes all new documentation - see https://looselab.github.io/readfish - and will prevent users from making many common mistakes.
> [!NOTE]
> Important: The TOML file specification has been modified for this version and users should update their TOML files accordingly.
This includes a description of the new plugin framework, developed by alexomics , which will enable users to develop their own custom mappers, squiggle analysis packages and other tools and then integrate them into a common readfish environment.
In principle readfish can be used as a library by other packages.
Full information on new features can be found in the readme and associated documentation. All issues should be reported by the GitHub issue tracker and not by email to the authors.
What's Changed
* Add unblock all script by alexomics
* Add github worklflow action to close stale issues by Adoni5
* Move logger initialisation into check that we have arguments by Adoni5
* Add pre commit and make all files compliant by Adoni5
* validation script by alexomics
* Switching behaviour of validate by mattloose
* Add readfish identifier to appear in guppy server logs by mattloose
* Feature/describe plugin by Adoni5
* Remove --chunk-log option by alexomics
* Implement runsafe and additional logging. by mattloose
* Implementing check on basecalling model in guppy plugin. This will va… by mattloose
* Fixes to describe by Adoni5
* Update _config.py to check barcodes if regions and barcodes are present. by Adoni5
* Enabling changes to the log for the readuntil client by tools which u… by mattloose
* Add `readfish[mappy,guppy]` as default install target by Adoni5
* Split mappy plugins by alexomics
* Feature/summarise-entry-point by Adoni5
* Fix-stats-macos-aarch-test by Adoni5
* Adding a check for the current break_reads_seconds value and testing … by mattloose
* Feature/logging-stats-padding by Adoni5
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