Release 2.2.0
Release 2.2.0
Breaking changes 💣 💔🙈
Autometa's autometa-taxonomy
and autometa-binning-summary
entrypoints (instead of taking --ncbi
as an input parameter) now take --dbdir
and --dbtype
to allow the user to use either the NCBI or GTDB database.
Command | 💔 Previous 💔 | 💚 New 💚 |
---|---|---|
autometa-taxonomy |
--ncbi |
--dbdir <ncbi-database-dirpath> , --dbtype ncbi (choices: ncbi, gtdb) |
autometa-binning-summary |
--ncbi |
--dbdir <ncbi-database-dirpath> , --dbtype ncbi (choices: ncbi, gtdb) |
NOTE: For implementation details for integrating other taxonomy databases see #284
🐚 Additional autometa workflows
- Addition of workflow where only required inputs are reads and assembly
autometa.sh
andautometa-large-data-mode.sh
now requiretaxa_routine
as an input parameter (choices are"ncbi"
or"ncbi_gtdb"
. Autometa workflow now contains an optional sub-workflow where binning is guided by GTDB taxonomy after retrieving bacteria and archaea classified using the NCBI database.
TaxonomyDatabase
🐍 GTDB taxonomy integration to use within Autometa's taxon-binning and genome-binning workflows.
For more information on GTDB database setup see the Autometa GTDB database documentation
(autometa) evan@userserver:~/Autometa$ autometa-setup-gtdb -h
usage: autometa-setup-gtdb [-h] --reps-faa REPS_FAA --dbdir DBDIR [--cpus CPUS]
optional arguments:
-h, --help show this help message and exit
--reps-faa REPS_FAA Path to directory containing GTDB ref genome animo acid data sequences. Can be tarballed.
--dbdir DBDIR Path to output GTDB database directory
--cpus CPUS Number of cpus to use for diamond-formatting GTDB database
TL;DR
Abstraction of taxonomy databases using TaxonomyDatabase
abstract base class with required abstractmethods
.
This is currently implemented for both the NCBI and GTDB taxonomy database. Future taxonomy database integrations should follow the format from the TaxonomyDatabase
class.
CAMI formatter
Binning validation/benchmarking utilities added/updated such as formatting autometa binning results into biobox format
Misc
- 💚 Fix pytest requirements in GH actions
- 🐛⬇️ pin
scipy
andjoblib
to avoidhdbscan
import error - 🐍🤫 Fix deprecated pandas method invocation in
bedtools.py
What's Changed
- 📝 Added contribution documentation by @jason-c-kwan in #277
- 🎨🐍 Add CAMI formatter entrypoint
autometa-cami-format
by @WiscEvan in #276 - 🎨🐍 Update deprecated pandas method invocation by @WiscEvan in #279
- ⬇️ 💚 force scipy==1.8 by @kaw97 in #286
- 🐚 New bash files for Autometa workflow by @samche42 in #281
- ⬆️ 🎨 Allow the use of gtdb taxonomy in Autometa by @Sidduppal in #284
- Add
--average-method
parameter toautometa-benchmark
by @WiscEvan in #290 - GTDB integration by @Sidduppal and @WiscEvan in #284
New Contributors
- @jason-c-kwan made their first contribution in #277
- @kaw97 made their first contribution in #286
Full Changelog: 2.1.0...2.2.0