Merge pull request galaxyproject#439 from clsiguret/amr_gene_detection

Add 'AMR gene detection' workflow

workflows/bacterial_genomics/amr_gene_detection/.dockstore.yml

@@ -0,0 +1,19 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /amr_gene_detection.ga
+  testParameterFiles:
+  - /amr_gene_detection-tests.yml
+  authors:
+  - name: ABRomics
+    email: mailto:[email protected]
+  - name: abromics-consortium
+    url: https://www.abromics.fr/
+  - name: Pierre Marin
+    alternateName: pimarin
+    orcid: 0000-0002-8304-138X
+  - name: Clea Siguret
+    alternateName: clsiguret
+    orcid: 0009-0005-6140-0379

workflows/bacterial_genomics/amr_gene_detection/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## [1.0] - 05-06-2024
+
+- First release

workflows/bacterial_genomics/amr_gene_detection/README.md

@@ -0,0 +1,30 @@
+# AMR gene detection workflow in an assembled bacterial genome (v1.0)
+
+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
+        - **AMRFinderPlus** to find antimicrobial resistance genes and point mutations 
+    - Virulence gene identification:
+        - **ABRicate** with VFDB_A database
+2. Aggregating outputs into a single JSON file
+    - **ToolDistillator** to extract and aggregate information from different tool outputs to JSON parsable files
+
+## Inputs
+
+1. Assembled bacterial genome in fasta format.
+
+## Outputs
+
+1. Genomic detection
+    - Antimicrobial resistance gene identification:
+        - AMR gene list
+        - MLST typing
+        - Plasmid gene identification
+        - Blast hits
+        - AMR gene fasta (assembled nucleotide sequences)
+        - Point mutation list
+    - Virulence gene identification:
+        - Gene identification in tabular format
+2. Aggregating outputs:
+    - JSON file with information about the outputs of **staramr**, **AMRFinderPlus**, **ABRicate**

workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml

@@ -0,0 +1,62 @@
+- doc: Test outline for amr_gene_detection.ga
+  job:
+    Input sequence fasta:
+      class: File
+      path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
+  outputs:
+    staramr_detailed_summary:
+        assert:
+        has_text:
+          text: "Resistance"
+        has_n_columns:
+          n: 12
+    staramr_resfinder_report:
+        assert:
+        has_text:
+          text: "tetracycline"
+        has_n_columns:
+          n: 13
+    staramr_mlst_report:
+      assert:
+        has_text:
+          text: "efaecalis"
+        has_n_columns:
+          n: 10
+    staramr_plasmidfinder_report:
+      assert:
+        has_text:
+          text: "CP002494"
+        has_n_columns:
+          n: 9
+    staramr_summary:
+      assert:
+        has_text:
+          text: "streptomycin"
+        has_n_columns:
+          n: 12
+    amrfinderplus_report:
+      assert:
+        has_text:
+          text: "Enterococcus faecalis quinolone resistant ParC"
+        has_n_columns:
+          n: 23
+    amrfinderplus_mutation:
+      assert:
+        has_text:
+          text: "cardiolipin synthase Cls"
+        has_n_columns:
+          n: 23
+    abricate_virulence_report:
+      assert:
+        has_text:
+          text: "endocarditis specific antigen"
+        has_n_columns:
+          n: 15
+    tooldistillator_summarize:
+      assert:
+        has_text:
+          text: "% Identity to reference sequence"
+        has_text:
+          text: "Enterococcus faecalis V583"
+        has_text:
+          text: "CGE Predicted Phenotype"