Updating bacterial_genomics/amr_gene_detection from 1.1.5 to 1.1.6

workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md

@@ -1,8 +1,20 @@
 # Changelog
 
-## [1.1.5] - 2024-10-21
+## [1.1.6] 2025-06-18
+
+### Manual update
+
+- `toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3`
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1`
+- `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1`
+- Adds 2 input parameters : StarAMR database and species selection (PointFinder)
+- Changes output name/tag for Tooldistillator
+- Fixes syntax and parameter errors
+
+## [1.1.5] 2024-10-21
 
 ### Automatic update
+
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1`
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy1`
 
@@ -15,6 +27,7 @@
 ## [1.1.3] - 2024-09-30
 
 ### Automatic update
+
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0`
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+galaxy0`
 
@@ -27,13 +40,14 @@
 ## [1.1.1] - 2024-07-08
 
 ### Automatic update
+
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0`
 - `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.8.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9+galaxy0`
 
 ## [1.1] - 2024-06-24
 
 ### Automatic update
+
 - `toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.10.0+galaxy1`
 
 ## [1.0] - 05-06-2024
-

workflows/bacterial_genomics/amr_gene_detection/README.md

@@ -1,9 +1,9 @@
-# AMR gene detection workflow in an assembled bacterial genome (v1.0)
+# AMR gene detection workflow in an assembled bacterial genome
 
 This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:
 1. Genomic detection
     - Antimicrobial resistance gene identification:
-        - **staramr** to blast against ResFinder and PlasmidFinder database
+        - **StarAMR** to blast against ResFinder, PointFinder and PlasmidFinder database
         - **AMRFinderPlus** to find antimicrobial resistance genes and point mutations 
     - Virulence gene identification:
         - **ABRicate** with VFDB_A database
@@ -27,4 +27,4 @@ This workflow uses assembled bacterial genome fasta files (but can be any fasta
     - Virulence gene identification:
         - Gene identification in tabular format
 2. Aggregating outputs:
-    - JSON file with information about the outputs of **staramr**, **AMRFinderPlus**, **ABRicate**
+    - JSON file with information about the outputs of **StarAMR**, **AMRFinderPlus**, **ABRicate**

workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml

@@ -2,10 +2,12 @@
   job:
     Input sequence fasta:
       class: File
-      path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
+      path: https://zenodo.org/records/15696987/files/shovill_contigs_fasta_contig00089.fasta
     Select a taxonomy group point mutation: Enterococcus_faecalis
     Select a AMR genes detection database: amrfinderplus_V3.12_2024-05-02.2
     Select a virulence genes detection database: vfdb
+    Select a StarmAMR database: staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502
+    Select species for point mutation analysis using PointFinder: enterococcus_faecalis
   outputs:
     staramr_detailed_summary:
         asserts:
@@ -16,50 +18,52 @@
     staramr_resfinder_report:
         asserts:
           has_text:
-            text: "tetracycline"
+            text: "Chloramphenicol"
           has_n_columns:
             n: 13
     staramr_mlst_report:
       asserts:
         has_text:
-          text: "efaecalis"
+          text: "Scheme"
+    staramr_pointfinder_report:
+      asserts:
+        has_text:
+          text: "Pointfinder Position"
         has_n_columns:
-          n: 10
+          n: 18
     staramr_plasmidfinder_report:
       asserts:
         has_text:
-          text: "CP002494"
+          text: "rep7a"
         has_n_columns:
           n: 9
     staramr_summary:
       asserts:
         has_text:
-          text: "streptomycin"
+          text: "erythromycin"
         has_n_columns:
           n: 12
     amrfinderplus_report:
       asserts:
         has_text:
-          text: "Enterococcus faecalis quinolone resistant ParC"
+          text: "catA"
         has_n_columns:
           n: 23
     amrfinderplus_mutation:
       asserts:
         has_text:
-          text: "cardiolipin synthase Cls"
+          text: "Element subtype"
         has_n_columns:
           n: 23
     abricate_virulence_report:
       asserts:
         has_text:
-          text: "endocarditis specific antigen"
-        has_n_columns:
-          n: 15
-    tooldistillator_summarize:
+          text: "RESISTANCE"
+    tooldistillator_summarize_amr:
       asserts:
         - that: "has_text"
           text: "% Identity to reference sequence"
         - that: "has_text"
-          text: "Enterococcus faecalis V583"
+          text: "pointfinder_file"
         - that: "has_text"
-          text: "Fibrinogen binding protein"
+          text: "LINCOSAMIDE"