Update MAGs workflow to 0.4

workflows/microbiome/mags-building/CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [0.4] - 2025-10-07
+
+### Manual updates
+
+* **metaSPAdes** now supports running in single-assembly mode when individual samples are submitted. Previously, it always performed co-assembly, which is the default tool setting.
+* **bakta**, **quast** (for the bins), **coverM** results are joined into one overview table each
+* For **dRep** also the clustering results are generated.
+* All tools have been updated to their latest versions.
+* Workflow annotations.
+
 ## [0.3] - 2025-06-09
 
 ### Automatic update

workflows/microbiome/mags-building/MAGs-generation-tests.yml

@@ -1,26 +1,20 @@
 - doc: Test for Metagenome-Assembled-Genomes-(MAGs)-generation
   job:
-    Trimmed reads from grouped samples:
+    Trimmed reads:
       class: Collection
       collection_type: list:paired
       elements:
       - class: Collection
         type: paired
         identifier: 50contig_reads
         elements:
-        - class: File
-          identifier: forward
-          location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
-          hashes:
-          - hash_function: SHA-1
-            hash_value: 0ee81cd4a9503acea42b8de5f28ad57cdc4b8f38
-        - class: File
-          identifier: reverse
-          location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
-          hashes:
-          - hash_function: SHA-1
-            hash_value: 2a4ad06c93902e25274ef9c026feb7168f089b57
-    Trimmed reads:
+          - class: File
+            identifier: forward
+            location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
+          - class: File
+            identifier: reverse
+            location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
+    Trimmed reads from grouped samples:
       class: Collection
       collection_type: list:paired
       elements:
@@ -31,17 +25,11 @@
         - class: File
           identifier: forward
           location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
-          hashes:
-          - hash_function: SHA-1
-            hash_value: 0ee81cd4a9503acea42b8de5f28ad57cdc4b8f38
         - class: File
           identifier: reverse
           location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
-          hashes:
-          - hash_function: SHA-1
-            hash_value: 2a4ad06c93902e25274ef9c026feb7168f089b57
     Choose Assembler: MEGAHIT
-    Custom Assemblies:
+    Custom Assemblies: null
     Minimum length of contigs to output: '200'
     Read length (CONCOCT): '100'
     Environment for the built-in model (SemiBin): global