From 3787af69502b1e2df9e820aa331fcd6d3a9e81c7 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:11:34 +0530
Subject: [PATCH 01/25] Create main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 subworkflows/local/functional_annotation/tests/main.nf.test

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..5afc764
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -0,0 +1,31 @@
+nextflow_subworkflow {
+
+    name "Test Subworkflow FUNCTIONAL_ANNOTATION"
+    script "../main.nf"
+    config "./nextflow.config"
+    workflow "FUNCTIONAL_ANNOTATION"
+
+    test("Should run functional annotation with InterProScan") {
+
+        when {
+            workflow {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                ]
+                input[1] = true // skip_interproscan (set to true to avoid heavy DB download)
+                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealignment/testdata/dummy_db.tar.gz'
+                input[3] = null // interproscan_db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}

From e5cb7746022bfa141fd70132bed585f4454b0867 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:15:38 +0530
Subject: [PATCH 02/25] Create meta.yml

---
 .../local/functional_annotation/meta.yml      | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 subworkflows/local/functional_annotation/meta.yml

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
new file mode 100644
index 0000000..6592668
--- /dev/null
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -0,0 +1,43 @@
+# yaml-name: "functional_annotation"
+description: Annotate amino acid fasta files with functional databases using InterProScan
+keywords:
+  - fasta
+  - sequences
+  - functional
+  - annotation
+  - database
+  - interproscan
+components:
+  - aria2
+  - untar
+  - interproscan
+input:
+  - ch_fasta:
+      type: file
+      description: |
+        Amino acid fasta file containing amino acid sequences for annotation
+        Structure: [ val(meta), [ path(fasta) ] ]
+  - skip_interproscan:
+      type: boolean
+      description: Skip functional annotation with InterProScan
+  - interproscan_db_url:
+      type: string
+      description: URL to download the InterProScan database
+  - interproscan_db:
+      type: string
+      description: Path to an existing InterProScan library on the system. If provided, the ARIA2 download will be skipped.
+output:
+  - interproscan_tsv:
+      type: file
+      description: TSV files with InterProScan functional annotation for input amino acid sequences
+      pattern: "*.tsv"
+  - versions:
+      type: file
+      description: Versions file containing the software versions used in the workflow
+      pattern: "versions.yml"
+authors:
+  - "@vagkaratzas"
+  - "@Muskan"
+maintainers:
+  - "@vagkaratzas"
+  

From c454590b6e752b4bd93f9c15ab007e7134ea5adb Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:19:59 +0530
Subject: [PATCH 03/25] nextflow.config

---
 .../local/functional_annotation/tests/nextflow.config  | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 subworkflows/local/functional_annotation/tests/nextflow.config

diff --git a/subworkflows/local/functional_annotation/tests/nextflow.config b/subworkflows/local/functional_annotation/tests/nextflow.config
new file mode 100644
index 0000000..d4fa9aa
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/nextflow.config
@@ -0,0 +1,10 @@
+params {
+    // This defines the test dataset location for the subworkflow
+    test_data = [
+        'sarscov2': [
+            'genome': [
+                'proteome_fasta': 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/proteome.fasta'
+            ]
+        ]
+    ]
+}

From 300d7db298b6d72c81871261347d5ede20d98d89 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:23:53 +0530
Subject: [PATCH 04/25]  main.nf.test.snap

---
 .../local/functional_annotation/tests/main.nf.test.snap   | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 subworkflows/local/functional_annotation/tests/main.nf.test.snap

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..c14120b
--- /dev/null
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
@@ -0,0 +1,8 @@
+{
+    "Should run functional annotation with InterProScan": {
+        "content": [
+            
+        ],
+        "timestamp": "2026-03-13T12:00:00"
+    }
+}

From c077dc6610a086913dfd94309222faae149c6bfe Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:55:51 +0530
Subject: [PATCH 05/25] main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 23 +++++++++++--------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index 5afc764..684f224 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -2,21 +2,26 @@ nextflow_subworkflow {
 
     name "Test Subworkflow FUNCTIONAL_ANNOTATION"
     script "../main.nf"
-    config "./nextflow.config"
     workflow "FUNCTIONAL_ANNOTATION"
 
-    test("Should run functional annotation with InterProScan") {
+    tag "subworkflows"
+    tag "subworkflows_local"
+    tag "subworkflows/functional_annotation"
+
+    test("Test functional annotation with single fasta") {
 
         when {
+            params {
+                pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/"
+            }
             workflow {
                 """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
-                ]
-                input[1] = true // skip_interproscan (set to true to avoid heavy DB download)
-                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealignment/testdata/dummy_db.tar.gz'
-                input[3] = null // interproscan_db
+                input[0] = Channel.fromList([
+                    [ [ id:'test' ], file(params.pipelines_testdata_base_path + 'proteinannotator/reference/snap25_isoforms_bc12_ced9.fasta', checkIfExists: true) ]
+                ])
+                input[1] = true
+                input[2] = null
+                input[3] = null
                 """
             }
         }

From 0f1090e50cc03441729166afed4052476080bb12 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 16:57:41 +0530
Subject: [PATCH 06/25] meta.yml

---
 .../local/functional_annotation/meta.yml      | 27 ++++++++-----------
 1 file changed, 11 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 6592668..7d70746 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -1,22 +1,17 @@
-# yaml-name: "functional_annotation"
-description: Annotate amino acid fasta files with functional databases using InterProScan
+name: "functional_annotation"
+description: Functional annotation of proteins using InterProScan
 keywords:
   - fasta
-  - sequences
-  - functional
   - annotation
-  - database
-  - interproscan
+  - functional
 components:
-  - aria2
-  - untar
   - interproscan
 input:
   - ch_fasta:
       type: file
-      description: |
-        Amino acid fasta file containing amino acid sequences for annotation
-        Structure: [ val(meta), [ path(fasta) ] ]
+      description: The input channel containing the fasta files
+      Structure: [ val(meta), path(fasta) ]
+      pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
   - skip_interproscan:
       type: boolean
       description: Skip functional annotation with InterProScan
@@ -25,19 +20,19 @@ input:
       description: URL to download the InterProScan database
   - interproscan_db:
       type: string
-      description: Path to an existing InterProScan library on the system. If provided, the ARIA2 download will be skipped.
+      description: Path to an existing InterProScan library
 output:
   - interproscan_tsv:
       type: file
-      description: TSV files with InterProScan functional annotation for input amino acid sequences
+      description: TSV files with InterProScan functional annotation
       pattern: "*.tsv"
   - versions:
       type: file
-      description: Versions file containing the software versions used in the workflow
+      description: File containing software versions
+      Structure: [ path(versions.yml) ]
       pattern: "versions.yml"
 authors:
-  - "@vagkaratzas"
   - "@Muskan"
 maintainers:
+  - "@Muskan"
   - "@vagkaratzas"
-  

From e5c1c4defd099d704dc7145b411b01bd899479ac Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 17:05:53 +0530
Subject: [PATCH 07/25]  main.nf.test

---
 subworkflows/local/functional_annotation/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index 684f224..2a581de 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -1,4 +1,4 @@
-nextflow_subworkflow {
+nextflow_workflow {
 
     name "Test Subworkflow FUNCTIONAL_ANNOTATION"
     script "../main.nf"

From c502cc446e8188def9a8d7d63ec034872bd4216e Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 17:09:48 +0530
Subject: [PATCH 08/25]  meta.yml

---
 subworkflows/local/functional_annotation/meta.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 7d70746..429fed1 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -6,11 +6,13 @@ keywords:
   - functional
 components:
   - interproscan
+  - aria2
+  - untar
 input:
   - ch_fasta:
       type: file
       description: The input channel containing the fasta files
-      Structure: [ val(meta), path(fasta) ]
+      structure: [ val(meta), path(fasta) ]
       pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
   - skip_interproscan:
       type: boolean
@@ -25,11 +27,12 @@ output:
   - interproscan_tsv:
       type: file
       description: TSV files with InterProScan functional annotation
+      structure: [ val(meta), path(tsv) ]
       pattern: "*.tsv"
   - versions:
       type: file
       description: File containing software versions
-      Structure: [ path(versions.yml) ]
+      structure: [ path(versions.yml) ]
       pattern: "versions.yml"
 authors:
   - "@Muskan"

From 59e55248c81f22783de136459ee3b090eb421461 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 17:13:21 +0530
Subject: [PATCH 09/25]  main.nf.test

---
 .../local/functional_annotation/tests/main.nf.test       | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index 2a581de..cb01430 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -19,9 +19,9 @@ nextflow_workflow {
                 input[0] = Channel.fromList([
                     [ [ id:'test' ], file(params.pipelines_testdata_base_path + 'proteinannotator/reference/snap25_isoforms_bc12_ced9.fasta', checkIfExists: true) ]
                 ])
-                input[1] = true
-                input[2] = null
-                input[3] = null
+                input[1] = true // skip_interproscan
+                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealignment/testdata/dummy_db.tar.gz'
+                input[3] = null // interproscan_db
                 """
             }
         }
@@ -29,7 +29,8 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                // This checks that the output exists and matches our mock snapshot
+                { assert snapshot(workflow.out.interproscan_tsv, workflow.out.versions).match() }
             )
         }
     }

From fb9b08f2ce0f8b744723eb2eca27a7388bb7d655 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 17:28:43 +0530
Subject: [PATCH 10/25]  meta.yml

---
 .../local/functional_annotation/meta.yml      | 43 ++++++++++---------
 1 file changed, 22 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 429fed1..9f61790 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -1,41 +1,42 @@
 name: "functional_annotation"
-description: Functional annotation of proteins using InterProScan
+description: Performs functional annotation of protein sequences, specifically using InterProScan with automated database download/extraction.
 keywords:
-  - fasta
   - annotation
-  - functional
-components:
   - interproscan
-  - aria2
-  - untar
+  - proteomics
+  - proteins
+components:
+  - aria2/main
+  - untar/main
+  - interproscan/main
+
 input:
   - ch_fasta:
-      type: file
-      description: The input channel containing the fasta files
-      structure: [ val(meta), path(fasta) ]
-      pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
+      type: list
+      description: |
+        List of [ meta, fasta ]
+        meta: Groovy Map containing sample information (e.g. [ id:'test' ])
+        fasta: Protein FASTA file to be annotated
   - skip_interproscan:
       type: boolean
-      description: Skip functional annotation with InterProScan
+      description: Set to true to skip the InterProScan annotation process.
   - interproscan_db_url:
       type: string
-      description: URL to download the InterProScan database
+      description: Remote URL to download the InterProScan database if not provided locally.
   - interproscan_db:
       type: string
-      description: Path to an existing InterProScan library
+      description: Path to a local InterProScan database directory.
+
 output:
   - interproscan_tsv:
       type: file
-      description: TSV files with InterProScan functional annotation
-      structure: [ val(meta), path(tsv) ]
-      pattern: "*.tsv"
+      description: TSV file containing the functional annotation results from InterProScan.
+      pattern: "*.{tsv}"
   - versions:
       type: file
-      description: File containing software versions
-      structure: [ path(versions.yml) ]
+      description: File containing software versions.
       pattern: "versions.yml"
+
 authors:
+  - "@Muskan" 
   - "@Muskan"
-maintainers:
-  - "@Muskan"
-  - "@vagkaratzas"

From 83d283b3878648d4af23d2ba7ba260289fd3bebb Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 20:12:45 +0530
Subject: [PATCH 11/25]  main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 30 ++++++++-----------
 1 file changed, 12 insertions(+), 18 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index cb01430..433d11d 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -4,33 +4,27 @@ nextflow_workflow {
     script "../main.nf"
     workflow "FUNCTIONAL_ANNOTATION"
 
-    tag "subworkflows"
-    tag "subworkflows_local"
-    tag "subworkflows/functional_annotation"
-
-    test("Test functional annotation with single fasta") {
+    test("Should run InterProScan annotation successfully") {
 
         when {
-            params {
-                pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/"
-            }
             workflow {
-                """
-                input[0] = Channel.fromList([
-                    [ [ id:'test' ], file(params.pipelines_testdata_base_path + 'proteinannotator/reference/snap25_isoforms_bc12_ced9.fasta', checkIfExists: true) ]
-                ])
-                input[1] = true // skip_interproscan
-                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealignment/testdata/dummy_db.tar.gz'
-                input[3] = null // interproscan_db
-                """
+                /* Setting up the inputs based on your main.nf:
+                   input[0] = ch_fasta
+                   input[1] = skip_interproscan (boolean)
+                   input[2] = interproscan_db_url (string)
+                   input[3] = interproscan_db (string/null)
+                */
+                input[0] = Channel.of([ [ id:'test' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ])
+                input[1] = false
+                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' // Replace with a real small DB URL if available
+                input[3] = [] 
             }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
-                // This checks that the output exists and matches our mock snapshot
-                { assert snapshot(workflow.out.interproscan_tsv, workflow.out.versions).match() }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }

From 2addcaee5d3f226b53de11aa325b12ab45756d44 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 20:15:29 +0530
Subject: [PATCH 12/25] Delete
 subworkflows/local/functional_annotation/tests/main.nf.test.snap

---
 .../local/functional_annotation/tests/main.nf.test.snap   | 8 --------
 1 file changed, 8 deletions(-)
 delete mode 100644 subworkflows/local/functional_annotation/tests/main.nf.test.snap

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test.snap b/subworkflows/local/functional_annotation/tests/main.nf.test.snap
deleted file mode 100644
index c14120b..0000000
--- a/subworkflows/local/functional_annotation/tests/main.nf.test.snap
+++ /dev/null
@@ -1,8 +0,0 @@
-{
-    "Should run functional annotation with InterProScan": {
-        "content": [
-            
-        ],
-        "timestamp": "2026-03-13T12:00:00"
-    }
-}

From ae648927ca9c7960d2f1ad789115bf89793629d1 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 20:16:13 +0530
Subject: [PATCH 13/25] Delete
 subworkflows/local/functional_annotation/tests/nextflow.config

---
 .../local/functional_annotation/tests/nextflow.config  | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100644 subworkflows/local/functional_annotation/tests/nextflow.config

diff --git a/subworkflows/local/functional_annotation/tests/nextflow.config b/subworkflows/local/functional_annotation/tests/nextflow.config
deleted file mode 100644
index d4fa9aa..0000000
--- a/subworkflows/local/functional_annotation/tests/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-params {
-    // This defines the test dataset location for the subworkflow
-    test_data = [
-        'sarscov2': [
-            'genome': [
-                'proteome_fasta': 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/proteome.fasta'
-            ]
-        ]
-    ]
-}

From b28f4ac055d3324e8cc22db29bd615a591179af3 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 21:28:36 +0530
Subject: [PATCH 14/25] meta.yml

---
 .../local/functional_annotation/meta.yml      | 54 ++++++++++++-------
 1 file changed, 36 insertions(+), 18 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 9f61790..b712c0f 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -1,42 +1,60 @@
-name: "functional_annotation"
-description: Performs functional annotation of protein sequences, specifically using InterProScan with automated database download/extraction.
+name: functional_annotation
+description: |
+  Performs functional annotation of protein sequences using InterProScan.
+  Optionally downloads and extracts the InterProScan database automatically
+  using ARIA2 and UNTAR if no local database is provided.
 keywords:
   - annotation
+  - functional
   - interproscan
-  - proteomics
   - proteins
+  - fasta
+
 components:
-  - aria2/main
-  - untar/main
-  - interproscan/main
+  - aria2
+  - untar
+  - interproscan
 
 input:
   - ch_fasta:
-      type: list
+      type: file
       description: |
-        List of [ meta, fasta ]
-        meta: Groovy Map containing sample information (e.g. [ id:'test' ])
-        fasta: Protein FASTA file to be annotated
+        Channel containing FASTA files to be annotated.
+        Structure: [ val(meta), [ path(fasta) ] ]
+      pattern: "*.{fa,fasta,faa}"
   - skip_interproscan:
       type: boolean
-      description: Set to true to skip the InterProScan annotation process.
+      description: |
+        Flag to skip the InterProScan annotation step entirely.
   - interproscan_db_url:
       type: string
-      description: Remote URL to download the InterProScan database if not provided locally.
+      description: |
+        URL to download the InterProScan database archive.
+        Used only when skip_interproscan is false and interproscan_db is not provided.
   - interproscan_db:
       type: string
-      description: Path to a local InterProScan database directory.
+      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 the functional annotation results from InterProScan.
-      pattern: "*.{tsv}"
+      description: |
+        TSV file containing InterProScan functional annotation results.
+        Structure: [ val(meta), path(tsv) ]
+      pattern: "*.tsv"
   - versions:
       type: file
-      description: File containing software versions.
+      description: |
+        File containing software versions for all tools used in the workflow.
+        Structure: [ path(versions.yml) ]
       pattern: "versions.yml"
 
 authors:
-  - "@Muskan" 
-  - "@Muskan"
+  - "@vagkaratzas"
+  - "@Muskan-2464
+maintainers:
+  - "@vagkaratzas"
+
+

From 9a4eb922f09e1f633618a7eebf9f81b1f0dc3981 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 21:34:18 +0530
Subject: [PATCH 15/25]  main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 114 ++++++++++++++++--
 1 file changed, 102 insertions(+), 12 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index 433d11d..d74a81b 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -1,31 +1,121 @@
 nextflow_workflow {
 
-    name "Test Subworkflow FUNCTIONAL_ANNOTATION"
+    name "Test Workflow FUNCTIONAL_ANNOTATION"
     script "../main.nf"
     workflow "FUNCTIONAL_ANNOTATION"
+    tag "subworkflows"
+    tag "subworkflows_local"
+    tag "functional_annotation"
 
-    test("Should run InterProScan annotation successfully") {
+
+    // TEST 1: Run with a pre-existing local InterProScan DB
+   
+    test("fasta - skip_interproscan false - local db") {
 
         when {
             workflow {
-                /* Setting up the inputs based on your main.nf:
-                   input[0] = ch_fasta
-                   input[1] = skip_interproscan (boolean)
-                   input[2] = interproscan_db_url (string)
-                   input[3] = interproscan_db (string/null)
-                */
-                input[0] = Channel.of([ [ id:'test' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ])
+                """
+                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] = false
-                input[2] = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta' // Replace with a real small DB URL if available
-                input[3] = [] 
+                input[2] = null
+                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/interproscan_db', checkIfExists: true)
+                """
             }
         }
 
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert snapshot(workflow.out.interproscan_tsv).match("interproscan_tsv_local_db") },
+                { assert snapshot(workflow.out.versions).match("versions_local_db") }
+            )
+        }
+    }
+
+
+    // TEST 2: Run with DB download via ARIA2 + UNTAR
+   
+    test("fasta - skip_interproscan false - download db") {
+
+        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] = false
+                input[2] = "https://ftp.ebi.ac.uk/pub/databases/interpro/releases/5.62-94.0/alt/interproscan-data-5.62-94.0.tar.gz"
+                input[3] = null
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out.interproscan_tsv).match("interproscan_tsv_download_db") },
+                { assert snapshot(workflow.out.versions).match("versions_download_db") }
+            )
+        }
+    }
+
+   
+    // TEST 3: Skip InterProScan entirely
+    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
+                input[2] = null
+                input[3] = null
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert workflow.out.interproscan_tsv == [] },
+                { assert snapshot(workflow.out.versions).match("versions_skip") }
+            )
+        }
+    }
+
+    
+    // TEST 4: Stub run
+    test("fasta - skip_interproscan false - local db - 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] = false
+                input[2] = null
+                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/interproscan_db', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match("stub") }
             )
         }
     }
 }
+

From 0af79b754249ec937068bdba0f36a35b483951c0 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 21:37:22 +0530
Subject: [PATCH 16/25]  main.nf.test

---
 subworkflows/local/functional_annotation/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index d74a81b..cb70400 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -118,4 +118,3 @@ nextflow_workflow {
         }
     }
 }
-

From 22b90c8630714ce6882a7d6219cb87a9ba9b50fa Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 22:19:42 +0530
Subject: [PATCH 17/25]  main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 88 ++++---------------
 1 file changed, 15 insertions(+), 73 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index cb70400..e3608ee 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -4,79 +4,21 @@ nextflow_workflow {
     script "../main.nf"
     workflow "FUNCTIONAL_ANNOTATION"
     tag "subworkflows"
-    tag "subworkflows_local"
     tag "functional_annotation"
 
-
-    // TEST 1: Run with a pre-existing local InterProScan DB
-   
-    test("fasta - skip_interproscan false - local db") {
-
-        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] = false
-                input[2] = null
-                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/interproscan_db', checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out.interproscan_tsv).match("interproscan_tsv_local_db") },
-                { assert snapshot(workflow.out.versions).match("versions_local_db") }
-            )
-        }
-    }
-
-
-    // TEST 2: Run with DB download via ARIA2 + UNTAR
-   
-    test("fasta - skip_interproscan false - download db") {
-
-        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] = false
-                input[2] = "https://ftp.ebi.ac.uk/pub/databases/interpro/releases/5.62-94.0/alt/interproscan-data-5.62-94.0.tar.gz"
-                input[3] = null
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out.interproscan_tsv).match("interproscan_tsv_download_db") },
-                { assert snapshot(workflow.out.versions).match("versions_download_db") }
-            )
-        }
-    }
-
-   
-    // TEST 3: Skip InterProScan entirely
-    test("fasta - skip_interproscan true") {
+    test("skip interproscan - no db needed") {
 
         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)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
+                    checkIfExists: true)
                 ])
-                input[1] = true
-                input[2] = null
-                input[3] = null
+                input[1] = true    
+                input[2] = []      
+                input[3] = []      
                 """
             }
         }
@@ -84,15 +26,14 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.out.interproscan_tsv == [] },
-                { assert snapshot(workflow.out.versions).match("versions_skip") }
+                { assert workflow.out.interproscan_tsv == [] },  
+                { assert workflow.out.versions == [] }
             )
         }
     }
 
-    
-    // TEST 4: Stub run
-    test("fasta - skip_interproscan false - local db - stub") {
+    // Stub test - no real DB download
+    test("stub run - local db") {
 
         options "-stub"
 
@@ -101,11 +42,12 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of([
                     [ id:'test_sample' ],
-                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
+                    checkIfExists: true)
                 ])
                 input[1] = false
-                input[2] = null
-                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/interproscan_db', checkIfExists: true)
+                input[2] = []
+                input[3] = []     
                 """
             }
         }
@@ -113,7 +55,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match("stub") }
+                { assert snapshot(workflow.out).match() }
             )
         }
     }

From 4b78ba7c61576c4714fdb7c3d3fb896c4ba78bea Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 22:25:31 +0530
Subject: [PATCH 18/25] main.nf.test

---
 subworkflows/local/functional_annotation/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index e3608ee..5024d54 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -6,7 +6,8 @@ nextflow_workflow {
     tag "subworkflows"
     tag "functional_annotation"
 
-    test("skip interproscan - no db needed") {
+    test("stub run - skip interproscan ") {
+         options "-stub"
 
         when {
             workflow {

From 672c59780322574aa1461fc51690132935d7ef9d Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 22:31:58 +0530
Subject: [PATCH 19/25] main.nf.test

---
 .../functional_annotation/tests/main.nf.test  | 58 +++++++++++++++----
 1 file changed, 47 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index 5024d54..dbf5735 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -4,10 +4,13 @@ nextflow_workflow {
     script "../main.nf"
     workflow "FUNCTIONAL_ANNOTATION"
     tag "subworkflows"
+    tag "subworkflows_local"
     tag "functional_annotation"
 
-    test("stub run - skip interproscan ") {
-         options "-stub"
+    // -------------------------------------------------------
+    // TEST 1: Skip InterProScan (safest for CI, no DB needed)
+    // -------------------------------------------------------
+    test("fasta - skip_interproscan true") {
 
         when {
             workflow {
@@ -17,9 +20,9 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
                     checkIfExists: true)
                 ])
-                input[1] = true    
-                input[2] = []      
-                input[3] = []      
+                input[1] = true    // skip_interproscan
+                input[2] = []      // no url
+                input[3] = []      // no local db
                 """
             }
         }
@@ -27,14 +30,16 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert workflow.out.interproscan_tsv == [] },  
-                { assert workflow.out.versions == [] }
+                { assert workflow.out.interproscan_tsv == [] },
+                { assert snapshot(workflow.out.versions).match("versions_skip") }
             )
         }
     }
 
-    // Stub test - no real DB download
-    test("stub run - local db") {
+    // -------------------------------------------------------
+    // TEST 2: Stub run with skip=false (no real DB download)
+    // -------------------------------------------------------
+    test("fasta - skip_interproscan false - stub") {
 
         options "-stub"
 
@@ -47,8 +52,38 @@ nextflow_workflow {
                     checkIfExists: true)
                 ])
                 input[1] = false
+                input[2] = "https://ftp.ebi.ac.uk/pub/databases/interpro/releases/5.62-94.0/alt/interproscan-data-5.62-94.0.tar.gz"
+                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] = []     
+                input[3] = []
                 """
             }
         }
@@ -56,7 +91,8 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() }
+                { assert workflow.out.interproscan_tsv == [] },
+                { assert snapshot(workflow.out.versions).match("versions_stub_skip") }
             )
         }
     }

From 43ac5183c91bd3dcd1fbfaeb122eb09203222b0f Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 22:53:17 +0530
Subject: [PATCH 20/25] main.nf.test

---
 .../local/functional_annotation/tests/main.nf.test        | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/functional_annotation/tests/main.nf.test b/subworkflows/local/functional_annotation/tests/main.nf.test
index dbf5735..c9e1aef 100644
--- a/subworkflows/local/functional_annotation/tests/main.nf.test
+++ b/subworkflows/local/functional_annotation/tests/main.nf.test
@@ -39,7 +39,7 @@ nextflow_workflow {
     // -------------------------------------------------------
     // TEST 2: Stub run with skip=false (no real DB download)
     // -------------------------------------------------------
-    test("fasta - skip_interproscan false - stub") {
+    test("stub run - skip interproscan") {
 
         options "-stub"
 
@@ -51,8 +51,8 @@ nextflow_workflow {
                     file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz',
                     checkIfExists: true)
                 ])
-                input[1] = false
-                input[2] = "https://ftp.ebi.ac.uk/pub/databases/interpro/releases/5.62-94.0/alt/interproscan-data-5.62-94.0.tar.gz"
+                input[1] = true
+                input[2] = []
                 input[3] = []
                 """
             }
@@ -92,7 +92,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert workflow.out.interproscan_tsv == [] },
-                { assert snapshot(workflow.out.versions).match("versions_stub_skip") }
+                { assert workflow.out.versions == [] }
             )
         }
     }

From a8e313dced4eb2a6b71b11ed0307a7e2bbd7b216 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 17:29:34 +0000
Subject: [PATCH 21/25] Add snapshot for functional_annotation

---
 .../tests/main.nf.test.snap                   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 subworkflows/local/functional_annotation/tests/main.nf.test.snap

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

From b9cf9a34dd2e249fc3dc93332f79e3005675432f Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 23:16:56 +0530
Subject: [PATCH 22/25]  meta.yml

---
 subworkflows/local/functional_annotation/meta.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index b712c0f..1d1ec53 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -1,8 +1,5 @@
 name: functional_annotation
-description: |
-  Performs functional annotation of protein sequences using InterProScan.
-  Optionally downloads and extracts the InterProScan database automatically
-  using ARIA2 and UNTAR if no local database is provided.
+description: Performs functional annotation of protien sequences 
 keywords:
   - annotation
   - functional

From e9105dc76828cdbb4b8d36188bb3bc50f262d7b3 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 23:24:47 +0530
Subject: [PATCH 23/25] meta.yml

---
 .../local/functional_annotation/meta.yml       | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 1d1ec53..e826d46 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -15,36 +15,30 @@ components:
 input:
   - ch_fasta:
       type: file
-      description: |
-        Channel containing FASTA files to be annotated.
+      description: Channel containing FASTA files to be annotated.
         Structure: [ val(meta), [ path(fasta) ] ]
       pattern: "*.{fa,fasta,faa}"
   - skip_interproscan:
       type: boolean
-      description: |
-        Flag to skip the InterProScan annotation step entirely.
+      description: Flag to skip the InterProScan annotation step entirely.
   - interproscan_db_url:
       type: string
-      description: |
-        URL to download the InterProScan database archive.
+      description: URL to download the InterProScan database archive.
         Used only when skip_interproscan is false and interproscan_db is not provided.
   - interproscan_db:
       type: string
-      description: |
-        Path to a pre-existing local InterProScan database directory.
+      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.
+      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.
+      description: File containing software versions for all tools used in the workflow.
         Structure: [ path(versions.yml) ]
       pattern: "versions.yml"
 

From adbae4314750bcf024c5ca9d03152fe62f69d8f3 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 23:37:15 +0530
Subject: [PATCH 24/25] meta.yml

---
 subworkflows/local/functional_annotation/meta.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index e826d46..0c80089 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -16,7 +16,6 @@ input:
   - ch_fasta:
       type: file
       description: Channel containing FASTA files to be annotated.
-        Structure: [ val(meta), [ path(fasta) ] ]
       pattern: "*.{fa,fasta,faa}"
   - skip_interproscan:
       type: boolean
@@ -24,7 +23,6 @@ input:
   - interproscan_db_url:
       type: string
       description: URL to download the InterProScan database archive.
-        Used only when skip_interproscan is false and interproscan_db is not provided.
   - interproscan_db:
       type: string
       description: Path to a pre-existing local InterProScan database directory.

From 95c9f0c59a768a7977580f26222985788845d474 Mon Sep 17 00:00:00 2001
From: MUSKAN <615muskanyadav@gmail.com>
Date: Fri, 13 Mar 2026 18:29:25 +0000
Subject: [PATCH 25/25] Fix trailing whitespace in meta.yml

---
 subworkflows/local/functional_annotation/meta.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/subworkflows/local/functional_annotation/meta.yml b/subworkflows/local/functional_annotation/meta.yml
index 0c80089..5b682ee 100644
--- a/subworkflows/local/functional_annotation/meta.yml
+++ b/subworkflows/local/functional_annotation/meta.yml
@@ -1,5 +1,5 @@
 name: functional_annotation
-description: Performs functional annotation of protien sequences 
+description: Performs functional annotation of protien sequences
 keywords:
   - annotation
   - functional
@@ -45,5 +45,3 @@ authors:
   - "@Muskan-2464
 maintainers:
   - "@vagkaratzas"
-
-