Update CHANGELOG.md

CHANGELOG.md

@@ -4,14 +4,18 @@
 
 - Added support for translation tables different than 11 to UniprotFinder and AlleleCallEvaluator.
 
+- Added check for legacy schemas that include files terminating in `bsr.txt`. The AlleleCall module warns users that the schema needs to be adapted and exits.
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 - Changed the `max_targets` value in UniprotFinder to avoid BLASTp warning when aligning schema representative alleles against proteomes.
 
-- Updated Dockerfile. Using pip to install chewBBACA instead of downloading source from GitHub.
+- Fixed an issue in the AlleleCallEvaluator module when using `--no-pa` and `--no-dm`.
 
-- Fixed an issue in AlleleCallEvaluator when using `--no-pa` and `--no-dm`.
+- The AlleleCallEvaluator module no longer tries to compute the distance matrix, MSA, and tree if cgMLST is composed of 0 loci.
 
 - Fixed an issue in RemoveGenes where it would not get the first ID in the input list.
 
+- Updated Dockerfile. Using pip to install chewBBACA instead of downloading source from GitHub.
+
 ## 3.3.5 - 2024-04-18
 
 - Added function to check if input files passed to the CreateSchema and AlleleCall modules have unique prefixes longer than 30 characters (the prefix includes everything in the basename before the first `.`). The process prints a message with the list of input files with a prefix longer than 30 characters and exits.