Merge pull request galaxyproject#441 from clsiguret/bacterial_genome_…

…annotation

Add 'Bacterial genome annotation' workflow

workflows/bacterial_genomics/bacterial_genome_annotation/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /bacterial_genome_annotation.ga
+  testParameterFiles:
+  - /bacterial_genome_annotation-tests.yml
+  authors:
+  - name: ABRomics
+    email: [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/bacterial_genome_annotation/CHANGELOG.md

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+# Changelog
+
+## [1.0] - 14-06-2024
+
+- First release

workflows/bacterial_genomics/bacterial_genome_annotation/README.md

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+# Bacterial genome annotation workflow (v1.0)
+
+This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:
+1. Genomic annotation
+    - **Bakta** to predict CDS and small proteins (sORF)
+2. Integron identification
+    - **IntegronFinder2** to identify CALIN elements, In0 elements, and complete integrons
+3. Plasmid gene identification
+    - **Plasmidfinder** to identify and typing plasmid sequences
+4. Inserted sequence (IS) detection
+    - **ISEScan** to detect IS elements
+5. 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 annotation:
+    - genome annotation in tabular, gff and several other formats
+    - annotation plot
+    - nucleotide and protein sequences identified
+    - summary of genomic identified elements
+2. Integron identification:
+    - integron identification in tabular format and a summary
+3. Plasmid gene identification:
+    - plasmid gene identified and associated blast hits
+4. Inserted Element (IS) detection:
+    - IS element list in tabular format
+    - is hits in fasta format
+    - ORF hits in protein and nucleotide fasta format
+    - IS annotation gff format
+5. Aggregating outputs:
+    - JSON file with information about the outputs of **Bakta**, **IntegronFinder2**, **Plasmidfinder**, **ISEScan**

workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml

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+- doc: Test outline for bacterial_genome_annotation.ga
+  job:
+    Input sequence fasta:
+      class: File
+      path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
+    Select a plasmid detection database: plasmidfinder_81c11f4_2023_12_04
+    Select a bacterial genome annotation database: V5.0_2023-02-20
+    Select a AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2
+  outputs:
+    integronfinder2_logfile_text:
+      assert:
+        has_text:
+          text: "Writing out results for replicon"
+    integronfinder2_summary:
+      assert:
+        has_n_columns:
+          n: 6
+    integronfinder2_results_tabular:
+      assert:
+        has_n_columns:
+          n: 14
+    bakta_hypothetical_tabular:
+      assert:
+        has_n_columns:
+          n: 9
+    bakta_annotation_json:
+      assert:
+        has_text:
+          text: "aa_hexdigest"
+    bakta_annotation_tabular:
+      assert:
+        has_n_columns:
+          n: 9
+    isescan_results_tabular:
+      assert:
+        has_n_columns:
+          n: 24
+    isescan_summary_tabular:
+      assert:
+        has_text:
+          text: "nIS"
+    isescan_logfile_text:
+      assert:
+        has_text:
+          text: "Both complete and partial IS elements are reported."
+    plasmidfinder_result_json:
+      assert:
+        has_text:
+          text: "positions_in_contig"
+    plasmidfinder_results_tabular:
+      assert:
+        has_n_columns:
+          n: 8
+    tooldistillator_summarize:
+      assert:
+        has_text:
+          text: "CDS12738(DOp1)"
+        has_text:
+          text: "CALIN"
+        has_text:
+          text: "insertion_sequence"