Update bacterial_genome_annotation WF

workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.2.1] 2026-02-07
+
+- User can decide if Tooldistillator should run or not (with and without Bakta)
+- Bakta output is feed to MultiQC
+- Bakta output will be formatted such that the annotation result are showed together for each inputted sequence in one file 
+
 ## [1.2.0] 2025-12-04
 
 ### Automatic update

workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml

@@ -1,69 +1,111 @@
 - doc: Test outline for bacterial_genome_annotation.ga
   job:
-    Input sequence fasta:
-      class: File
-      path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
-      hashes:
-      - hash_function: SHA-1
-        hash_value: b77e9cf8473eaba8a640a398a0b06b9c87249052
+    Sequence collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: test_input
+        location: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
+        hashes:
+        - hash_function: SHA-1
+          hash_value: b77e9cf8473eaba8a640a398a0b06b9c87249052
     Plasmid detection database: plasmidfinder_81c11f4_2023_12_04
     Bacterial genome annotation database: V5.0_2023-02-20
     AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2
     Run Bakta : true
+    Run ToolDistillator without bakta: true
+    Run ToolDistillator with only bakta: true
   outputs:
     integronfinder2_logfile_text:
-      asserts:
-        has_text:
-          text: "Writing out results for replicon"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "Writing out results for replicon"
     integronfinder2_summary:
-      asserts:
-        has_text:
-          text: "contig00001"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "contig00001"
     integronfinder2_results_tabular:
-      asserts:
-        has_text:
-          text: "contig00009_42"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "contig00009_42"
     bakta_hypothetical_tabular:
-      asserts:
-        has_text:
-          text: "DHJLLP_04750"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "DHJLLP_04750"
     bakta_annotation_json:
-      asserts:
-        has_text:
-          text: "aa_hexdigest"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "aa_hexdigest"
     bakta_annotation_tabular:
-      asserts:
-        has_text:
-          text: "Phosphotransferase system cellobiose-specific component IIC"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "Phosphotransferase system cellobiose-specific component IIC"
     isescan_results_tabular:
-      asserts:
-        has_text:
-          text: "IS256_162"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "IS256_162"
     isescan_summary_tabular:
-      asserts:
-        has_text:
-          text: "nIS"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "nIS"
     isescan_logfile_text:
-      asserts:
-        has_text:
-          text: "Both complete and partial IS elements are reported."
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "Both complete and partial IS elements are reported."
     plasmidfinder_result_json:
-      asserts:
-        has_text:
-          text: "positions_in_contig"
+      element_tests:
+        test_input:
+          asserts:
+            has_text:
+              text: "positions_in_contig"
     plasmidfinder_results_tabular:
-      asserts:
-        has_n_columns:
-          n: 8
+      element_tests:
+        test_input:
+          asserts:
+            has_n_columns:
+              n: 8
     tooldistillator_summarize_annotation_without_bakta:
+      element_tests:
+        test_input:
+          asserts:
+          - that: "has_text"
+            text: "contig00009"
+          - that: "has_text"
+            text: "rep9b:WARNING"
+    tooldistillator_summarize_bakta:
+      element_tests:
+        test_input:
+          asserts:
+          - that: "has_text"
+            text: "UniParc:UPI000005C018"
+          - that: "has_text"
+            text: "GO:0050511"
+    bakta_cut_annotation_summary:
       asserts:
       - that: "has_text"
-        text: "contig00009"
+        text: "Annotation"
       - that: "has_text"
-        text: "rep9b:WARNING"
-    tooldistillator_summarize_bakta:
+        text: "CDSs"
+    multiqc_html_report:
       asserts:
       - that: "has_text"
-        text: "UniParc:UPI000005C018"
-      - that: "has_text"
-        text: "GO:0050511"
+        text: "bakta"