Stopped forcing eutheria_odb10

We will fix that properly in #100

CHANGELOG.md

@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] [2024-02-26]
+
+### Enhancements & fixes
+
+- Stopped forcing the `eutheria_odb10` BUSCO lineage to be used for all mammals.
+  This to synchronise this pipeline with the [BlobToolKit pipeline](https://github.com/sanger-tol/blobtoolkit).
+
 ## [[1.1.0](https://github.com/sanger-tol/genomenote/releases/tag/1.1.0)] - Golden Retriever - [2024-01-04]
 
 ### Enhancements & fixes

CITATION.cff

@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/genomenote v1.1.0
+title: sanger-tol/genomenote v1.1.1
 message: >-
     If you use this software, please cite it using the
     metadata from this file.
@@ -34,5 +34,5 @@ identifiers:
 repository-code: "https://github.com/sanger-tol/genomenote"
 license: MIT
 commit: TODO
-version: 1.1.0
+version: 1.1.1
 date-released: "2022-10-07"

bin/get_odb.py

@@ -47,10 +47,8 @@ def get_odb(ncbi_summary, lineage_tax_ids, file_out):
     # Do the intersection to find the ancestors that have a BUSCO lineage
     odb_arr = [lineage_tax_ids_dict[taxon_id] for taxon_id in ancestor_taxon_ids if taxon_id in lineage_tax_ids_dict]
 
-    # The most recent [-1] OBD10 lineage is selected, unless one of the lineage values is "eutheria", then choose "eutheria"
-    # NOTE: this rule is a guess that hasn't been confirmed by Karen
-    odb_val = "eutheria_odb10" if "eutheria_odb10" in odb_arr else odb_arr[-1]
-
+    # The most recent [-1] OBD10 lineage is selected
+    odb_val = odb_arr[-1]
     out_dir = os.path.dirname(file_out)
     make_dir(out_dir)
 

nextflow.config

@@ -221,7 +221,7 @@ manifest {
     description     = """Creating standarised genome assembly publications"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.1.0'
+    version         = '1.1.1'
     doi             = '10.5281/zenodo.7949384'
 }