diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/.dockstore.yml b/workflows/bacterial_genomics/bacterial_genome_annotation/.dockstore.yml
new file mode 100644
index 000000000..009a2f9ef
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/.dockstore.yml
@@ -0,0 +1,19 @@
+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: abromics-support@groupes.france-bioinformatique.fr
+  - 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
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md
new file mode 100644
index 000000000..7e0b1137f
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+
+## [1.0] - 14-06-2024
+
+- First release
\ No newline at end of file
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/README.md b/workflows/bacterial_genomics/bacterial_genome_annotation/README.md
new file mode 100644
index 000000000..2b685e657
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/README.md
@@ -0,0 +1,36 @@
+# 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**
\ No newline at end of file
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml
new file mode 100644
index 000000000..96a7fc4de
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml
@@ -0,0 +1,61 @@
+- 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"
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga
new file mode 100644
index 000000000..72e788846
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation.ga
@@ -0,0 +1,1199 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.",
+    "creator": [
+        {
+            "class": "Person",
+            "email": "mailto:abromics-support@groupes.france-bioinformatique.fr",
+            "name": "ABRomics"
+        },
+        {
+            "class": "Organization",
+            "name": "abromics-consortium",
+            "url": "https://www.abromics.fr/"
+        },
+        {
+            "alternateName": "pimarin",
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0002-8304-138X",
+            "name": "Pierre Marin",
+            "alternateName": "pimarin"
+        },
+        {
+            "alternateName": "clsiguret",
+            "class": "Person",
+            "identifier": "https://orcid.org/0009-0005-6140-0379",
+            "name": "Clea Siguret",
+            "alternateName": "clsiguret"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "GPL-3.0-or-later",
+    "release": "1.0",
+    "name": "bacterial_genome_annotation",
+    "steps": {
+        "0": {
+            "annotation": "Can be any fasta file.",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Can be any fasta file.",
+                    "name": "Input sequence fasta"
+                }
+            ],
+            "label": "Input sequence fasta",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 559.2197431502472
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "8afa880e-a04c-4831-b37b-d0f317f767b0",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Select a database to identify plasmids with PlasmidFinder.",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Select a database to identify plasmids with PlasmidFinder.",
+                    "name": "Select a plasmid detection database"
+                }
+            ],
+            "label": "Select a plasmid detection database",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 9.602014342350742,
+                "top": 734.3939210886799
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"plasmidfinder_81c11f4_2023_12_04\", \"restrictions\": [\"plasmidfinder_314d85f_2023_03_17\",\"81c11f4_2023_12_04/\"], \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "66c11ad1-7cd5-40b7-b97f-8d15cc097dd9",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "a2d4e531-c070-45c1-b56a-be4356aabc79"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "Select a database to predict CDS and small proteins (sORF) with Bakta.",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Select a database to predict CDS and small proteins (sORF) with Bakta.",
+                    "name": "Select a bacterial genome annotation database"
+                }
+            ],
+            "label": "Select a bacterial genome annotation database",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 21.882601498378413,
+                "top": 859.5166625976562
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"V5.1_2024-01-19\", \"restrictions\": [\"V5.0light_2023-02-20\", \"V5.0_2023-02-20\", \"V5.1_2024-01-19\"], \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "4de1f52c-078c-4112-86ad-e4e8f3b62e3a",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "724dc1d5-6f90-4c1c-915c-99dded697740"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "Selecting this database is not necessary if the bacterial genome database (with Bakta) version is greater than 5.0.",
+            "content_id": null,
+            "errors": null,
+            "id": 3,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Selecting this database is not necessary if the bacterial genome database (with Bakta) version is greater than 5.0.",
+                    "name": "Select a AMRFinderPlus database"
+                }
+            ],
+            "label": "Select a AMRFinderPlus database",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 10.643158620281753,
+                "top": 995.2631409484753
+            },
+            "tool_id": null,
+            "tool_state": "{\"default\": \"amrfinderplus_V3.12_2024-05-02.2\", \"restrictions\": [\"amrfinderplus_V3.12_2024-05-02.2\"], \"parameter_type\": \"text\", \"optional\": true}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "aec02a2c-6bf7-476d-91aa-3f1ce49083c7",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "768e962a-f016-41c6-96c5-4b32b26b4856"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "genomic_annotation_insertionelement_isescan",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "input_file": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "genomic_annotation_insertionelement_isescan",
+            "name": "ISEScan",
+            "outputs": [
+                {
+                    "name": "logfile",
+                    "type": "txt"
+                },
+                {
+                    "name": "summary",
+                    "type": "tabular"
+                },
+                {
+                    "name": "all_results",
+                    "type": "tabular"
+                },
+                {
+                    "name": "annotation",
+                    "type": "gff"
+                },
+                {
+                    "name": "is_fasta",
+                    "type": "fasta"
+                },
+                {
+                    "name": "orf_fna",
+                    "type": "fasta"
+                },
+                {
+                    "name": "orf_faa",
+                    "type": "fasta"
+                }
+            ],
+            "position": {
+                "left": 887.7889628790149,
+                "top": 105.14125185095409
+            },
+            "post_job_actions": {
+                "RenameDatasetActionall_results": {
+                    "action_arguments": {
+                        "newname": "isescan_results_tabular"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "all_results"
+                },
+                "RenameDatasetActionannotation": {
+                    "action_arguments": {
+                        "newname": "isescan_annotation_gff3"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "annotation"
+                },
+                "RenameDatasetActionis_fasta": {
+                    "action_arguments": {
+                        "newname": "isescan_is_fasta"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "is_fasta"
+                },
+                "RenameDatasetActionlogfile": {
+                    "action_arguments": {
+                        "newname": "isescan_logfile_text"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "logfile"
+                },
+                "RenameDatasetActionorf_faa": {
+                    "action_arguments": {
+                        "newname": "isescan_orf_faa"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "orf_faa"
+                },
+                "RenameDatasetActionorf_fna": {
+                    "action_arguments": {
+                        "newname": "isescan_orf_fasta"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "orf_fna"
+                },
+                "RenameDatasetActionsummary": {
+                    "action_arguments": {
+                        "newname": "isescan_summary_tabular"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "summary"
+                },
+                "TagDatasetActionall_results": {
+                    "action_arguments": {
+                        "tags": "isescan_results_tabular"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "all_results"
+                },
+                "TagDatasetActionannotation": {
+                    "action_arguments": {
+                        "tags": "isescan_annotation_gff3"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "annotation"
+                },
+                "TagDatasetActionis_fasta": {
+                    "action_arguments": {
+                        "tags": "isescan_is_fasta"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "is_fasta"
+                },
+                "TagDatasetActionlogfile": {
+                    "action_arguments": {
+                        "tags": "isescan,logfile"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "logfile"
+                },
+                "TagDatasetActionorf_faa": {
+                    "action_arguments": {
+                        "tags": "isescan_orf_faa"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "orf_faa"
+                },
+                "TagDatasetActionorf_fna": {
+                    "action_arguments": {
+                        "tags": "isescan_orf_fasta"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "orf_fna"
+                },
+                "TagDatasetActionsummary": {
+                    "action_arguments": {
+                        "tags": "isescan_summary_tabular"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "summary"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "9e776e7fab4f",
+                "name": "isescan",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"log_activate\": true, \"remove_short_is\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.7.2.3+galaxy1",
+            "type": "tool",
+            "uuid": "f589af2f-9dd9-41c0-b7a2-a499c875cb54",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "isescan_summary_tabular",
+                    "output_name": "summary",
+                    "uuid": "a09e2ed7-5b31-4beb-9923-d5ec6910da16"
+                },
+                {
+                    "label": "isescan_annotation_gff3",
+                    "output_name": "annotation",
+                    "uuid": "de82533b-90f8-470d-80a2-e1559be93f0d"
+                },
+                {
+                    "label": "isescan_logfile_text",
+                    "output_name": "logfile",
+                    "uuid": "c0539e24-831e-406f-a5d2-3dd52845a5d7"
+                },
+                {
+                    "label": "isescan_results_tabular",
+                    "output_name": "all_results",
+                    "uuid": "24f7dee0-f50a-4444-83f4-b09623a4a993"
+                },
+                {
+                    "label": "isescan_orf_faa",
+                    "output_name": "orf_faa",
+                    "uuid": "c74754f5-e011-4f55-801f-feeab8dd777c"
+                },
+                {
+                    "label": "isescan_is_fasta",
+                    "output_name": "is_fasta",
+                    "uuid": "a89b0159-ccef-4c10-9b17-d5da62312bda"
+                },
+                {
+                    "label": "isescan_orf_fasta",
+                    "output_name": "orf_fna",
+                    "uuid": "1a91afd7-104d-4807-bffa-61c5df646b85"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "genomic_annotation_integron",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "sequence": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Integron Finder",
+                    "name": "topology_file"
+                }
+            ],
+            "label": "genomic_annotation_integron",
+            "name": "Integron Finder",
+            "outputs": [
+                {
+                    "name": "integron_log",
+                    "type": "txt"
+                },
+                {
+                    "name": "integrons_table",
+                    "type": "tsv"
+                },
+                {
+                    "name": "summary",
+                    "type": "tsv"
+                }
+            ],
+            "position": {
+                "left": 581.3510244512896,
+                "top": 719.4853608141518
+            },
+            "post_job_actions": {
+                "RenameDatasetActionintegron_log": {
+                    "action_arguments": {
+                        "newname": "integronfinder2_logfile_text"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "integron_log"
+                },
+                "RenameDatasetActionintegrons_table": {
+                    "action_arguments": {
+                        "newname": "integronfinder2_results_tabular"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "integrons_table"
+                },
+                "RenameDatasetActionsummary": {
+                    "action_arguments": {
+                        "newname": "integronfinder2_summary"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "summary"
+                },
+                "TagDatasetActionintegron_log": {
+                    "action_arguments": {
+                        "tags": "integronfinder,logfile"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "integron_log"
+                },
+                "TagDatasetActionintegrons_table": {
+                    "action_arguments": {
+                        "tags": "integronfinder2_results_tabular"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "integrons_table"
+                },
+                "TagDatasetActionsummary": {
+                    "action_arguments": {
+                        "tags": "integronfinder2_summary"
+                    },
+                    "action_type": "TagDatasetAction",
+                    "output_name": "summary"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/integron_finder/integron_finder/2.0.3+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "392f100eebcd",
+                "name": "integron_finder",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"gbk\": false, \"local_max\": true, \"no_logfile\": false, \"pdf\": false, \"promoter_attI\": true, \"sequence\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"attc_settings\": {\"dist_thresh\": \"4000\", \"calin_threshold\": \"2\", \"max_attc_size\": \"200\", \"min_attc_size\": \"40\", \"keep_palindromes\": false, \"covar_matrix\": {\"__class__\": \"RuntimeValue\"}}, \"protein_settings\": {\"no_proteins\": false, \"union_integrases\": false, \"func_annot\": false}}, \"topology_file\": {\"__class__\": \"RuntimeValue\"}, \"type_replicon\": null, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.0.3+galaxy0",
+            "type": "tool",
+            "uuid": "0f39c064-cac7-4ee7-9f37-94b7717a033e",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "integronfinder2_logfile_text",
+                    "output_name": "integron_log",
+                    "uuid": "dca60f87-9f7a-4631-b197-62ca54f7bafe"
+                },
+                {
+                    "label": "integronfinder2_summary",
+                    "output_name": "summary",
+                    "uuid": "b96d90c3-7678-41b8-9b01-61d5c9da80bc"
+                },
+                {
+                    "label": "integronfinder2_results_tabular",
+                    "output_name": "integrons_table",
+                    "uuid": "cb38191b-3a0e-43d3-823a-0c9563e39d66"
+                }
+            ]
+        },
+        "6": {
+            "annotation": "genomic_annotation_plasmid_plasmidfinder",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/plasmidfinder/2.1.6+galaxy1",
+            "errors": null,
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+}
\ No newline at end of file