Merge pull request #108 from sanger-tol/prod_fix

Stopped forcing eutheria_odb10

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)
 

conf/base.config

@@ -4,33 +4,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Increasing the number of CPUs often gives diminishing returns, so we increase it
-    following a logarithm curve. Example:
-        - 0 < value <= 1: start + step
-        - 1 < value <= 2: start + 2*step
-        - 2 < value <= 4: start + 3*step
-        - 4 < value <= 8: start + 4*step
-    In order to support re-runs, the step increase may be multiplied by the attempt
-    number prior to calling this function.
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-// Modified logarithm function that doesn't return negative numbers
-def positive_log(value, base) {
-    if (value <= 1) {
-        return 0
-    } else {
-        return Math.log(value)/Math.log(base)
-    }
-}
-
-def log_increase_cpus(start, step, value, base) {
-    return check_max(start + step * (1 + Math.ceil(positive_log(value, base))), 'cpus')
-}
-
-
 process {
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }

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'
 }
 
@@ -260,3 +260,30 @@ def check_max(obj, type) {
         }
     }
 }
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Increasing the number of CPUs often gives diminishing returns, so we increase it
+    following a logarithm curve. Example:
+        - 0 < value <= 1: start + step
+        - 1 < value <= 2: start + 2*step
+        - 2 < value <= 4: start + 3*step
+        - 4 < value <= 8: start + 4*step
+    In order to support re-runs, the step increase may be multiplied by the attempt
+    number prior to calling this function.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+// Modified logarithm function that doesn't return negative numbers
+def positive_log(value, base) {
+    if (value <= 1) {
+        return 0
+    } else {
+        return Math.log(value)/Math.log(base)
+    }
+}
+
+def log_increase_cpus(start, step, value, base) {
+    return check_max(start + step * (1 + Math.ceil(positive_log(value, base))), 'cpus')
+}
+