Clusty submodule updated (fixed issue with empty graphs after filtering).

Author: agudys

.github/workflows/large.yml

@@ -8,7 +8,7 @@ jobs:
  ########################################################################################
   checkout:
     name: Checkout
-    runs-on: [self-hosted, vclust, x64_linux, large]
+    runs-on: [self-hosted, x64_linux, large]
 
     steps:
     - name: clean
@@ -31,7 +31,7 @@ jobs:
     strategy:
       matrix:
         compiler: [14]
-    runs-on: [self-hosted, vclust, x64_linux, large]
+    runs-on: [self-hosted, x64_linux, large]
 
     steps:
 #    - name: clean
@@ -74,7 +74,7 @@ jobs:
       INPUT_DIR: ../../../../vclust/input
       TEMP_DIR: ../../../../vclust/temp
 
-    runs-on: [self-hosted, vclust, x64_linux, large] 
+    runs-on: [self-hosted, x64_linux, large] 
 
     steps:
     - name: prefilter
@@ -111,7 +111,7 @@ jobs:
       INPUT_DIR: ../../../../vclust/input
       TEMP_DIR: ../../../../vclust/temp
 
-    runs-on: [self-hosted, vclust, x64_linux, large] 
+    runs-on: [self-hosted, x64_linux, large] 
 
     steps:
     - name: cluster

3rd_party/clusty

@@ -96,7 +96,7 @@ The Vclust documentation is available on the [GitHub Wiki](https://github.com/re
 
 ## Citation
 
-Zielezinski A, Gudyś A, Barylski J, Siminski K, Rozwalak P, Dutilh BE, Deorowicz S. *Ultrafast and accurate sequence alignment and clustering of viral genomes*. bioRxiv [[doi:10.1101/2024.06.27.601020](https://www.biorxiv.org/content/10.1101/2024.06.27.601020)].
+Zielezinski A, Gudyś A, Barylski J, Siminski K, Rozwalak P, Dutilh BE, Deorowicz S. Ultrafast and accurate sequence alignment and clustering of viral genomes. Nat Methods. [https://doi.org/10.1038/s41592-025-02701-7](https://doi.org/10.1038/s41592-025-02701-7)
 
 ## License
 

3rd_party/kmer-db

@@ -16,11 +16,11 @@
 import tempfile
 import typing
 
-__version__ = '1.3.0'
+__version__ = '1.3.1'
 
-CITATION = '''Zielezinski A, Gudys A et al. (2024) 
+CITATION = '''Zielezinski A, Gudys A et al. (2025) 
 Ultrafast and accurate sequence alignment and clustering of viral genomes. 
-bioRxiv. doi: 10.1101/2024.06.27.601020'''
+Nat Methods. doi: https://doi.org/10.1038/s41592-025-02701-7'''
 
 DEFAULT_THREAD_COUNT = min(multiprocessing.cpu_count(), 64)