diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
new file mode 100644
index 0000000..5b682ee
--- /dev/null
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -0,0 +1,47 @@
+name: functional_annotation
+description: Performs functional annotation of protien sequences
+keywords:
+  - annotation
+  - functional
+  - interproscan
+  - proteins
+  - fasta
+
+components:
+  - aria2
+  - untar
+  - interproscan
+
+input:
+  - ch_fasta:
+      type: file
+      description: Channel containing FASTA files to be annotated.
+      pattern: "*.{fa,fasta,faa}"
+  - skip_interproscan:
+      type: boolean
+      description: Flag to skip the InterProScan annotation step entirely.
+  - interproscan_db_url:
+      type: string
+      description: URL to download the InterProScan database archive.
+  - interproscan_db:
+      type: string
+      description: Path to a pre-existing local InterProScan database directory.
+        If provided, skips the download and extraction steps.
+
+output:
+  - interproscan_tsv:
+      type: file
+      description: TSV file containing InterProScan functional annotation results.
+        Structure: [ val(meta), path(tsv) ]
+      pattern: "*.tsv"
+  - versions:
+      type: file
+      description: File containing software versions for all tools used in the workflow.
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+
+authors:
+  - "@vagkaratzas"
+  - "@Muskan-2464
+maintainers:
+  - "@vagkaratzas"
diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
new file mode 100644
index 0000000..c9e1aef
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -0,0 +1,99 @@
+nextflow_workflow {
+
+    name "Test Workflow FUNCTIONAL_ANNOTATION"
+    script "../main.nf"
+    workflow "FUNCTIONAL_ANNOTATION"
+    tag "subworkflows"
+    tag "subworkflows_local"
+    tag "functional_annotation"
+
+    // -------------------------------------------------------
+    // TEST 1: Skip InterProScan (safest for CI, no DB needed)
+    // -------------------------------------------------------
+    test("fasta - skip_interproscan true") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
+                    checkIfExists: true)
+                ])
+                input[1] = true    // skip_interproscan
+                input[2] = []      // no url
+                input[3] = []      // no local db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.interproscan_tsv == [] },
+                { assert snapshot(workflow.out.versions).match("versions_skip") }
+            )
+        }
+    }
+
+    // -------------------------------------------------------
+    // TEST 2: Stub run with skip=false (no real DB download)
+    // -------------------------------------------------------
+    test("stub run - skip interproscan") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
+                    checkIfExists: true)
+                ])
+                input[1] = true
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("stub") }
+            )
+        }
+    }
+
+    // -------------------------------------------------------
+    // TEST 3: Stub run - skip interproscan
+    // -------------------------------------------------------
+    test("fasta - skip_interproscan true - stub") {
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test_sample' ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
+                    checkIfExists: true)
+                ])
+                input[1] = true
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.interproscan_tsv == [] },
+                { assert workflow.out.versions == [] }
+            )
+        }
+    }
+}
diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test.snap b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
new file mode 100644
index 0000000..f4444ca
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "versions_skip": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-03-13T17:28:57.029553387"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "interproscan_tsv": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-03-13T17:29:04.51251929"
+    }
+}
\ No newline at end of file