Update MAGs workflow to 0.4

workflows/microbiome/mags-building/CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.4] - 2025-10-07
+
+### Logic Update
+
+* **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.
+* Grouping for grouped assemblies is now handled in the main workflow through a metadata sample sheet (`Metadata for grouped assembly/binning`). If no sample sheet is provided, individual assemblies are performed by default.
+* All tools have been updated to their latest versions.
+
 ## [0.3] - 2025-06-09
 
 ### Automatic update

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

@@ -1,19 +1,5 @@
 - doc: Test for Metagenome-Assembled-Genomes-(MAGs)-generation
   job:
-    Trimmed reads from grouped samples:
-      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
-          - class: File
-            identifier: reverse
-            location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
     Trimmed reads:
       class: Collection
       collection_type: list:paired
@@ -29,6 +15,7 @@
             identifier: reverse
             location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
     Choose Assembler: MEGAHIT
+    Metadata for grouped assembly/binning: null
     Custom Assemblies: null
     Minimum length of contigs to output: '200'
     Read length (CONCOCT): '100'