Closed evanroyrees closed 1 year ago
Base: 27.72% // Head: 27.62% // Decreases project coverage by -0.10%
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Release 2.20
🐚 Additional autometa workflows
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
:snake: GTDB taxonomy integration to use within Autometa's taxon-binning and genome-binning workflows.
TL;DR
Abstraction of taxonomy databases using
TaxonomyDatabase
abstract base class with requiredabstractmethods
.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
scipy
andjoblib
to avoidhdbscan
import errorbedtools.py