From 4ff89cbbeadc01b42d7867654f9a19d2e07850e3 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 10 Jun 2025 17:15:13 +0100
Subject: [PATCH 01/26] basic nf-test yml file

(cherry picked from commit fc744985cf2f011e5bb3353ce5af0345f486cf8c)
---
 nf-test.yaml | 47 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 nf-test.yaml

diff --git a/nf-test.yaml b/nf-test.yaml
new file mode 100644
index 0000000..335f491
--- /dev/null
+++ b/nf-test.yaml
@@ -0,0 +1,47 @@
+on:
+  # PRs and push to main
+  push:
+    branches:
+      - main
+  pull_request:
+    branches: 
+      - main
+name: Test nf-test installation
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    name: A test to install nf-test
+    strategy:
+      matrix:
+        NF-TEST_VER:
+          - "0.9.2"
+        with-pdiff:
+          - true
+          - false
+steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          cache: "npm"
+      - name: Install dependencies
+        run: npm ci
+      - name: Build
+        run: npm run build
+      - uses: actions/setup-java@v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - uses: nf-core/setup-nextflow@v2
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: nf-test install action step
+        uses: ./
+        with:
+          version: "${{ matrix.NF-TEST_VER }}"
+          install-pdiff: "${{ matrix.with-pdiff }}"
+      - name: Smoke test
+        run: nf-test version
\ No newline at end of file

From 21fc7958ea3b48f20928f052d219b440fe1d0898 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Wed, 11 Jun 2025 11:33:10 +0100
Subject: [PATCH 02/26] move nf-test.yaml under github dir

(cherry picked from commit 694cf0a125787f699d6f408b4876b25ec1c9d377)
---
 .github/workflows/nf-test.yaml | 47 ++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 .github/workflows/nf-test.yaml

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
new file mode 100644
index 0000000..335f491
--- /dev/null
+++ b/.github/workflows/nf-test.yaml
@@ -0,0 +1,47 @@
+on:
+  # PRs and push to main
+  push:
+    branches:
+      - main
+  pull_request:
+    branches: 
+      - main
+name: Test nf-test installation
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    name: A test to install nf-test
+    strategy:
+      matrix:
+        NF-TEST_VER:
+          - "0.9.2"
+        with-pdiff:
+          - true
+          - false
+steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+          cache: "npm"
+      - name: Install dependencies
+        run: npm ci
+      - name: Build
+        run: npm run build
+      - uses: actions/setup-java@v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - uses: nf-core/setup-nextflow@v2
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: nf-test install action step
+        uses: ./
+        with:
+          version: "${{ matrix.NF-TEST_VER }}"
+          install-pdiff: "${{ matrix.with-pdiff }}"
+      - name: Smoke test
+        run: nf-test version
\ No newline at end of file

From 87bab307d18082d829bd96995a592541d6b6509b Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Wed, 11 Jun 2025 12:07:16 +0100
Subject: [PATCH 03/26] update the nf-test.yaml to basic format

(cherry picked from commit 6b33ac792a7791f5707ce326b64f31089b3d544a)
---
 .github/workflows/nf-test.yaml | 61 ++++++++++++----------------------
 nf-test.yaml                   | 47 --------------------------
 2 files changed, 22 insertions(+), 86 deletions(-)
 delete mode 100644 nf-test.yaml

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index 335f491..45d1752 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -1,47 +1,30 @@
-on:
-  # PRs and push to main
-  push:
-    branches:
-      - main
-  pull_request:
-    branches: 
-      - main
-name: Test nf-test installation
+name: NF Tests
+on: [push, pull_request]
 jobs:
   test:
     runs-on: ubuntu-latest
-    name: A test to install nf-test
-    strategy:
-      matrix:
-        NF-TEST_VER:
-          - "0.9.2"
-        with-pdiff:
-          - true
-          - false
-steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-          cache: "npm"
-      - name: Install dependencies
-        run: npm ci
-      - name: Build
-        run: npm run build
-      - uses: actions/setup-java@v4
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
         with:
-          distribution: "temurin"
-          java-version: "17"
-      - uses: nf-core/setup-nextflow@v2
+          fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
         with:
-          python-version: "3.11"
+          java-version: '11'
+          distribution: 'adopt'
 
-      - name: nf-test install action step
-        uses: ./
+      - name: Setup Nextflow latest-edge
+        uses: nf-core/setup-nextflow@v1
         with:
-          version: "${{ matrix.NF-TEST_VER }}"
-          install-pdiff: "${{ matrix.with-pdiff }}"
-      - name: Smoke test
-        run: nf-test version
\ No newline at end of file
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests
+        run: nf-test test --ci #this is used to prevent updating the snapshot 
\ No newline at end of file
diff --git a/nf-test.yaml b/nf-test.yaml
deleted file mode 100644
index 335f491..0000000
--- a/nf-test.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-on:
-  # PRs and push to main
-  push:
-    branches:
-      - main
-  pull_request:
-    branches: 
-      - main
-name: Test nf-test installation
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    name: A test to install nf-test
-    strategy:
-      matrix:
-        NF-TEST_VER:
-          - "0.9.2"
-        with-pdiff:
-          - true
-          - false
-steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-          cache: "npm"
-      - name: Install dependencies
-        run: npm ci
-      - name: Build
-        run: npm run build
-      - uses: actions/setup-java@v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - uses: nf-core/setup-nextflow@v2
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-
-      - name: nf-test install action step
-        uses: ./
-        with:
-          version: "${{ matrix.NF-TEST_VER }}"
-          install-pdiff: "${{ matrix.with-pdiff }}"
-      - name: Smoke test
-        run: nf-test version
\ No newline at end of file

From b71deca77b1e4a54825d5437dfc9daa5bc25dab2 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Wed, 11 Jun 2025 15:45:49 +0100
Subject: [PATCH 04/26] update the version of nextflow

(cherry picked from commit cff3d46d82d9b3d74e3ca1975571a6716c2409b0)
---
 .github/workflows/nf-test.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index 45d1752..1b993b2 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -17,9 +17,9 @@ jobs:
           distribution: 'adopt'
 
       - name: Setup Nextflow latest-edge
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
-          version: "latest-edge"
+          version: "latest-stable"
 
       - name: Install nf-test
         run: |

From a16a0596acfd8d14eaa2edb0006d545888a15ebc Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Jun 2025 11:55:05 +0100
Subject: [PATCH 05/26] update nextflow version

(cherry picked from commit bb9f5a36d6c2e4d7dd3b7d76ad5266e060987be2)
---
 .github/workflows/nf-test.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index 1b993b2..c4bc9b0 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -16,7 +16,7 @@ jobs:
           java-version: '11'
           distribution: 'adopt'
 
-      - name: Setup Nextflow latest-edge
+      - name: Setup Nextflow latest
         uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-stable"

From 015c2095fc756f62dcc734bc7ff224e3f44fdbc3 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Feb 2026 14:32:51 +0000
Subject: [PATCH 06/26] update nf-test

---
 .github/workflows/nf-test.yaml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index c4bc9b0..a07b4e0 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -1,5 +1,10 @@
 name: NF Tests
 on: [push, pull_request]
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NFTEST_VER: "0.9.0"
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -11,7 +16,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '11'
           distribution: 'adopt'
@@ -22,9 +27,9 @@ jobs:
           version: "latest-stable"
 
       - name: Install nf-test
-        run: |
-          wget -qO- https://get.nf-test.com | bash
-          sudo mv nf-test /usr/local/bin/
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
 
       - name: Run Tests
         run: nf-test test --ci #this is used to prevent updating the snapshot 
\ No newline at end of file

From 021a9d19d4a69d3c0838245428c8009d1486c169 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Thu, 19 Feb 2026 12:35:04 +0000
Subject: [PATCH 07/26] added singularity

---
 .github/workflows/nf-test.yaml | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index a07b4e0..c7aff96 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -8,7 +8,14 @@ env:
 jobs:
   test:
     runs-on: ubuntu-latest
-
+    name: nf-tes
+    needs: [nf-test-changes]
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    strategy:
+      fail-fast: false
+      matrix:
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [singularity]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -31,5 +38,18 @@ jobs:
         with:
           version: ${{ env.NFTEST_VER }}
 
+      - name: Setup apptainer
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        with:
+          python-version: "3.11"
+
       - name: Run Tests
-        run: nf-test test --ci #this is used to prevent updating the snapshot 
\ No newline at end of file
+        run: nf-test test --ci --changed-since HEAD^ #this is used to prevent updating the snapshot 

From 7604ee9a804f45cca1ab95ec0bbf144316520bac Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Thu, 19 Feb 2026 12:36:28 +0000
Subject: [PATCH 08/26] correct nf-test

---
 .github/workflows/nf-test.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index c7aff96..0078a5b 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -52,4 +52,4 @@ jobs:
           python-version: "3.11"
 
       - name: Run Tests
-        run: nf-test test --ci --changed-since HEAD^ #this is used to prevent updating the snapshot 
+        run: nf-test test --ci #this is used to prevent updating the snapshot 

From ee0e8cf2e4beffccd4f01130f122980c917e89b9 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Thu, 19 Feb 2026 12:38:48 +0000
Subject: [PATCH 09/26] correct nf-test

---
 .github/workflows/nf-test.yaml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index 0078a5b..d7b570c 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -8,14 +8,7 @@ env:
 jobs:
   test:
     runs-on: ubuntu-latest
-    name: nf-tes
-    needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' )
-    strategy:
-      fail-fast: false
-      matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
-        profile: [singularity]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4

From 2fa42bb9784c45fa6553c2a13abb36dfeec4d612 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Fri, 13 Mar 2026 12:35:22 +0000
Subject: [PATCH 10/26] correct the linting

---
 modules/ensembl/annotation/dumpanno/meta.yml  | 48 ++++-----
 modules/ensembl/database/dbfactory/meta.yml   | 39 ++++----
 .../ensembl/download/assemblydata/meta.yml    | 45 ++++-----
 modules/ensembl/download/genbank/meta.yml     | 34 ++++---
 modules/ensembl/dump/genomestats/meta.yml     | 47 +++++----
 modules/ensembl/fasta/dumpfastanuc/meta.yml   | 53 ++++++----
 .../ensembl/fasta/dumpfastapeptide/meta.yml   | 53 ++++++----
 modules/ensembl/genbank/extractgb/meta.yml    | 98 ++++++++++++-------
 modules/ensembl/gff3/dumpgff3/meta.yml        | 53 ++++++----
 modules/ensembl/gff3/validation/meta.yml      | 53 +++++-----
 modules/ensembl/manifest/integrity/meta.yml   | 69 ++++++-------
 modules/ensembl/manifest/maker/meta.yml       | 49 +++-------
 12 files changed, 351 insertions(+), 290 deletions(-)

diff --git a/modules/ensembl/annotation/dumpanno/meta.yml b/modules/ensembl/annotation/dumpanno/meta.yml
index e474f32..8d6bd20 100644
--- a/modules/ensembl/annotation/dumpanno/meta.yml
+++ b/modules/ensembl/annotation/dumpanno/meta.yml
@@ -1,7 +1,8 @@
----
 name: "annotation_dumpanno"
 
-description: This module is used to dump the functional annotation of a genome from core databases.
+description:
+  This module is used to dump the functional annotation of a genome from
+  core databases.
 
 keywords:
   - container
@@ -9,42 +10,29 @@ keywords:
   - docker
   - ensembl-legacy-scripts
   - fasta
-  
+
 tools:
   - "annotation":
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      description: "This module handles all annotation-related interactions with the core database, including annotation dumping and processing"
-      license: ['Apache License version 2.0']
+      description:
+        "This module handles all annotation-related interactions with the\
+        \ core database, including annotation dumping and processing"
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
   # Only when we have meta
-  - meta:
-        type: map
-        description: |
-          A meta map including 'core database information'.
-          e.g. [ id:'db_name', server_details:[ host:'db' ] ]
-        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+  - - db: {}
 output:
-  - meta:
-      type: map
-      description: |
-        Database containing meta information.
-        e.g. [ id:'db_name', server_details:[ host:'db' ] ]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
-  - functional_annotation.json:
-      type: map
-      description: |
-        Functional annotation file containing biotypes.
-        e.g [ db:'database name', file("*.json") ]
-      pattern: ".json"
-
+  - functional_annotation:
+      - db: {}
+      - functional_annotation: {}
+      - "*.json": {}
   - versions:
-      type: file
-      description: File containing software versions.
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing software versions.
+          pattern: "versions.yml"
 authors:
   - "@ensembl-dev"
 maintainers:
diff --git a/modules/ensembl/database/dbfactory/meta.yml b/modules/ensembl/database/dbfactory/meta.yml
index d0cb82f..25f5444 100644
--- a/modules/ensembl/database/dbfactory/meta.yml
+++ b/modules/ensembl/database/dbfactory/meta.yml
@@ -1,6 +1,7 @@
----
 name: "database_dbfactory"
-description: Generate a list of one or more databases plus some associated meta table information.
+description:
+  Generate a list of one or more databases plus some associated meta table
+  information.
 
 keywords:
   - container
@@ -13,28 +14,28 @@ tools:
   - database:
       description: "Modules which function to read or write information from core databases."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - server:
-      type: map
-      description: "Groovy Map containing mysql server host, port, user and password 
-        meta and file of JSON database filter information."
-        e.g. [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
-  - filtermap:
-      type: map
-      description: "Prefix to filter core databases. [default: none]"
-
+  - - server:
+        type: map
+        description: >
+          Groovy Map containing mysql server host, port, user and password meta  and
+          file of JSON database filter information.
+          e.g. [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
+    - filter_map: {}
 output:
   - dbs_meta_json:
-      type: file
-      description: "JSON file containing database metadata."
-      pattern: "dbs.json"  
+      - dbs.json:
+          type: file
+          description: "JSON file containing database metadata."
+          pattern: "dbs.json"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/download/assemblydata/meta.yml b/modules/ensembl/download/assemblydata/meta.yml
index 0f93a86..63372ea 100644
--- a/modules/ensembl/download/assemblydata/meta.yml
+++ b/modules/ensembl/download/assemblydata/meta.yml
@@ -1,6 +1,7 @@
----
 name: "download_assemblydata"
-description: Generate a list of one or more databases plus some associated meta table information.
+description:
+  Generate a list of one or more databases plus some associated meta table
+  information.
 
 keywords:
   - ensembl-genomio
@@ -13,34 +14,28 @@ keywords:
 
 tools:
   - download:
-      description: "Modules which function to download information or various data from externally hosted resources."
+      description:
+        "Modules which function to download information or various data from\
+        \ externally hosted resources."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing A single INSDC GCA or NCBI 'amended' GCF genome assembly accession meta information.
-        e.g. `[ accession:'GCA_000000000.1' ]`
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing A single INSDC GCA or NCBI 'amended' GCF genome assembly accession meta information.
+          e.g. `[ accession:'GCA_000000000.1' ]`
 output:
-  - min_set:
-      type: map
-      description: "Groovy Map including various genome assembly data files (.txt, .fna, .gbff) into compressed Gzip archives."
-        e.g. [ accession:'GCA_000000000.1', file("*_assembly_report.txt"), file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
-      pattern: (*.txt, *.fna.gz, *.gbff.gz)
-  - opt_set:
-      type: map
-      description: "Groovy Map including various genome assembly data files (.txt, .faa, .gff) into compressed Gzip archives."
-        e.g. [ accession:'GCA_000000000.1', file("*_assembly_report.txt"), file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
-      pattern: (*.txt, *.fna.gz, *.gbff.gz)
+  - min_set: []
+  - opt_set: []
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/download/genbank/meta.yml b/modules/ensembl/download/genbank/meta.yml
index 79b8e31..151d5b9 100644
--- a/modules/ensembl/download/genbank/meta.yml
+++ b/modules/ensembl/download/genbank/meta.yml
@@ -1,4 +1,3 @@
----
 name: "download_genbank"
 description: Download a single sequence from NCBI GenBank.
 
@@ -12,27 +11,30 @@ keywords:
 
 tools:
   - download:
-      description: "Modules which function to download information or various data from externally hosted resources."
+      description:
+        "Modules which function to download information or various data from\
+        \ externally hosted resources."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - accession:
-      type: map
-      description: Meta map including sequence accession. Sequence record associated with 
-        NCBI accession (e.g. NC_0-9+, NM_0-9+, NT_0-9+, NP_0-9+)
-        e.g. [[ accession:'NC_12341']]
-
+  - - meta: {}
 output:
   - gb_sequence:
-      type: file
-      description: A sequence record outfile in genbank format.
-      pattern: "output.gb"
+      - meta:
+          type: file
+          description: A sequence record outfile in genbank format.
+          pattern: "output.gb"
+      - output.gb:
+          type: file
+          description: A sequence record outfile in genbank format.
+          pattern: "output.gb"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/dump/genomestats/meta.yml b/modules/ensembl/dump/genomestats/meta.yml
index 65ebf0a..1e69215 100644
--- a/modules/ensembl/dump/genomestats/meta.yml
+++ b/modules/ensembl/dump/genomestats/meta.yml
@@ -1,4 +1,3 @@
----
 name: "dump_genomestats"
 description: A module for dumping a core database
 keywords:
@@ -10,29 +9,41 @@ keywords:
 
 tools:
   - dump:
-      description: "Modules which function to dump various forms of data from a core database."
+      description:
+        "Modules which function to dump various forms of data from a core\
+        \ database."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - db:
-      type: map
-      description: "A meta map including 'core database name'."
-        e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+  - - db:
+        type: map
+        description: >
+          A meta map including 'core database name'.
+          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
+          ...]]
+          pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
 output:
   - core_stats:
-      type: map
-      description: "JSON file containing core database statistics (assembly and annotation)."
-        e.g [ db:"database name", file("core_stats.json") ]
-      pattern: "core_stats.json"
+      - db:
+          type: map
+          description: >
+            JSON file containing core database statistics (assembly and annotation).
+            e.g [ db:"database name", file("core_stats.json") ]
+            pattern: "core_stats.json"
+      - core_stats.json:
+          type: map
+          description: >
+            JSON file containing core database statistics (assembly and annotation).
+            e.g [ db:"database name", file("core_stats.json") ]
+            pattern: "core_stats.json"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/fasta/dumpfastanuc/meta.yml b/modules/ensembl/fasta/dumpfastanuc/meta.yml
index 09f29c1..0b6c504 100644
--- a/modules/ensembl/fasta/dumpfastanuc/meta.yml
+++ b/modules/ensembl/fasta/dumpfastanuc/meta.yml
@@ -1,4 +1,3 @@
----
 name: "fasta_dumpfastanuc"
 description: A module for dumping core database gene module nucleotide fasta seqs
 
@@ -12,29 +11,47 @@ keywords:
 
 tools:
   - "fasta":
-      description: "Modules which function to facilitate data deposition/retrieval of fasta sequences."
+      description:
+        "Modules which function to facilitate data deposition/retrieval of\
+        \ fasta sequences."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - db:
-      type: map
-      description: "A meta map including 'core database name'."
-        e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+  - - db:
+        type: map
+        description: >
+          A meta map including 'core database name'.
+          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
+          ...]]
+        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
 output:
   - nucleotide_fasta:
-      type: map
-      description: "Fasta file containing nucleotide sequence(s)."
-        e.g [ db:'database name', file("*_fasta_dna.fasta") ]
-      pattern: "*_fasta_dna.fasta"
+      - db:
+          type: map
+          description: >
+            Fasta file containing nucleotide sequence(s).
+            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
+          pattern: "*_fasta_dna.fasta"
+      - fasta_dna:
+          type: map
+          description: >
+            Fasta file containing nucleotide sequence(s).
+            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
+          pattern: "*_fasta_dna.fasta"
+      - "*.fasta":
+          type: map
+          description: >
+            Fasta file containing nucleotide sequence(s).
+            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
+          pattern: "*_fasta_dna.fasta"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/fasta/dumpfastapeptide/meta.yml b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
index a4f81eb..3a02fcb 100644
--- a/modules/ensembl/fasta/dumpfastapeptide/meta.yml
+++ b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
@@ -1,4 +1,3 @@
----
 name: "fasta_dumpfastapeptide"
 description: A module for dumping peptide FASTA sequences from core databases
 
@@ -12,29 +11,47 @@ keywords:
 
 tools:
   - "fasta":
-      description: "Modules which function to facilitate data deposition/retrieval of fasta sequences."
+      description:
+        "Modules which function to facilitate data deposition/retrieval of\
+        \ fasta sequences."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - db:
-      type: map
-      description: "A meta map including 'core database name'."
-        e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+  - - db:
+        type: map
+        description: >
+          A meta map including 'core database name'.
+          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
+          ...]]
+        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
 output:
   - peptide_fasta:
-      type: map
-      description: "Fasta file containing peptide sequence(s)."
-        e.g [ db:'database name', file("*_fasta_pep.fasta") ]
-      pattern: "*_fasta_pep.fasta"
+      - db:
+          type: map
+          description: >
+            Fasta file containing peptide sequence(s).
+            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
+          pattern: "*_fasta_pep.fasta"
+      - fasta_pep:
+          type: map
+          description: >
+            Fasta file containing peptide sequence(s).
+            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
+          pattern: "*_fasta_pep.fasta"
+      - "*.fasta":
+          type: map
+          description: >
+            Fasta file containing peptide sequence(s).
+            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
+          pattern: "*_fasta_pep.fasta"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/genbank/extractgb/meta.yml b/modules/ensembl/genbank/extractgb/meta.yml
index 9ddcd0f..172113b 100644
--- a/modules/ensembl/genbank/extractgb/meta.yml
+++ b/modules/ensembl/genbank/extractgb/meta.yml
@@ -1,6 +1,7 @@
----
 name: "genbank_extractgb"
-description: Parse a GenBank file and create cleaned up files and validate generated JSON files. 
+description:
+  Parse a GenBank file and create cleaned up files and validate generated
+  JSON files.
 
 keywords:
   - container
@@ -12,49 +13,76 @@ keywords:
 
 tools:
   - "genbank":
-      description: "Modules with functions related to work with Genbank related data files."
+      description:
+        "Modules with functions related to work with Genbank related data\
+        \ files."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing genome database meta information
-        e.g. `[ accession:'NC_XXXX.X' ]`
-  - gb_file:
-      type: file
-      description: |
-        File path to genbank formatted input file (*.gb)
-        e.g. `[gb_file("genome.gb")]`
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing genome database meta information
+          e.g. `[ accession:'NC_XXXX.X' ]`
+    - gb_file:
+        type: file
+        description: |
+          File path to genbank formatted input file (*.gb)
+          e.g. `[gb_file("genome.gb")]`
 output:
   - genome:
-      type: file
-      description: Genome metadata (JSON)
-      pattern: "genome.json"
+      - meta:
+          type: file
+          description: Genome metadata (JSON)
+          pattern: "genome.json"
+      - genome.json:
+          type: file
+          description: Genome metadata (JSON)
+          pattern: "genome.json"
   - seq_regions:
-      type: file
-      description: Sequence region(s) meta (JSON)
-      pattern: "seq_region.json"
+      - meta:
+          type: file
+          description: Sequence region(s) meta (JSON)
+          pattern: "seq_region.json"
+      - seq_region.json:
+          type: file
+          description: Sequence region(s) meta (JSON)
+          pattern: "seq_region.json"
   - dna_fasta:
-      type: file
-      description: Genome nucleotide sequence(s) (FASTA)
-      pattern: "dna.fasta"
+      - meta:
+          type: file
+          description: Genome nucleotide sequence(s) (FASTA)
+          pattern: "dna.fasta"
+      - dna.fasta:
+          type: file
+          description: Genome nucleotide sequence(s) (FASTA)
+          pattern: "dna.fasta"
   - gene_gff:
-      type: file
-      description: Gene model information (GFF3)
-      pattern: "*.gff"
+      - meta:
+          type: file
+          description: Gene model information (GFF3)
+          pattern: "*.gff"
+      - "*.gff":
+          type: file
+          description: Gene model information (GFF3)
+          pattern: "*.gff"
   - pep_fasta:
-      type: file
-      description: Genome protein-coding gene amino acid sequence(s) (FASTA)
-      pattern: "pep.fasta"
+      - meta:
+          type: file
+          description: Genome protein-coding gene amino acid sequence(s) (FASTA)
+          pattern: "pep.fasta"
+      - pep.fasta:
+          type: file
+          description: Genome protein-coding gene amino acid sequence(s) (FASTA)
+          pattern: "pep.fasta"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/gff3/dumpgff3/meta.yml b/modules/ensembl/gff3/dumpgff3/meta.yml
index 1d27a3c..2df6712 100644
--- a/modules/ensembl/gff3/dumpgff3/meta.yml
+++ b/modules/ensembl/gff3/dumpgff3/meta.yml
@@ -1,4 +1,3 @@
----
 name: "gff3_dumpgff3"
 description: write your description here
 
@@ -11,29 +10,47 @@ keywords:
 
 tools:
   - "gff3":
-      description: "Modules for GFF3 validation, data deposition and retrieval from/into GFF3 file format"
+      description:
+        "Modules for GFF3 validation, data deposition and retrieval from/into\
+        \ GFF3 file format"
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - db:
-      type: map
-      description: "A meta map including 'core database name'."
-        e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
-      pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
-
+  - - db:
+        type: map
+        description: >
+          A meta map including 'core database name'.
+          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
+          ...]]
+        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
 output:
   - gff3:
-      type: map
-      description: "GFF3 file containing gene model(s)."
-        e.g [ db:'database name', file("*.gff3") ]
-      pattern: "*.gff3"
+      - db:
+          type: map
+          description: >
+            GFF3 file containing gene model(s).
+            e.g [ db:'database name', file("*.gff3") ]
+          pattern: "*.gff3"
+      - gff3:
+          type: map
+          description: >
+            GFF3 file containing gene model(s).
+            e.g [ db:'database name', file("*.gff3") ]
+          pattern: "*.gff3"
+      - "*.gff3":
+          type: map
+          description: >
+            GFF3 file containing gene model(s).
+            e.g [ db:'database name', file("*.gff3") ]
+          pattern: "*.gff3"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/gff3/validation/meta.yml b/modules/ensembl/gff3/validation/meta.yml
index 344861b..0a18747 100644
--- a/modules/ensembl/gff3/validation/meta.yml
+++ b/modules/ensembl/gff3/validation/meta.yml
@@ -1,4 +1,3 @@
----
 name: "gff3_validation"
 description: Check for proper validation of the GFF3 using GenomeTools.
 
@@ -12,37 +11,39 @@ keywords:
 
 tools:
   - "gff3":
-      description: "Modules for GFF3 validation, data deposition and retrieval from/into GFF3 file format"
+      description:
+        "Modules for GFF3 validation, data deposition and retrieval from/into\
+        \ GFF3 file format"
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
-  
-  - gene_models:
-      type: file
-      description: GFF3 files
-      pattern: "*.{gff3}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ id:'accession1' ]`
+    - gene_models:
+        type: file
+        description: GFF3 files
+        pattern: "*.{gff3}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
   - gene_models:
-      type: file
-      description: All files used as entry
-      pattern: "*.{gff3}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - gene_models.gff3:
+          type: file
+          description: All files used as entry
+          pattern: "*.{gff3}"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/manifest/integrity/meta.yml b/modules/ensembl/manifest/integrity/meta.yml
index 44b8ec6..0f4df00 100644
--- a/modules/ensembl/manifest/integrity/meta.yml
+++ b/modules/ensembl/manifest/integrity/meta.yml
@@ -1,4 +1,3 @@
----
 name: "manifest_integrity"
 description: Check the data integrity of a set of genomic files, listed by their manifest.
 keywords:
@@ -12,45 +11,47 @@ tools:
   - "manifest":
       description: "Nextflow modules for genomic data file manifest comparison/checking"
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+      license: ["Apache License version 2.0"]
+      identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
-  - manifest_files:
-      type: file
-      description: Set of genomic data files
-      pattern: "*.{gff3,fasta,json}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ id:'accession1' ]`
+    - manifest_files:
+        type: file
+        description: Set of genomic data files
+        pattern: "*.{gff3,fasta,json}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
-
   - all_files:
-      type: file
-      description: All files used as entry.
-      pattern: "*.{gff3,fasta,json}"
-
-  - integrity_file:
-      type: file
-      description: Captures potential errors detected during the integrity check of a manifest file (manifest.json).
-      pattern: "integrity.out"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - '*.*", includeInputs: true':
+          type: file
+          description: All files used as entry.
+          pattern: "*.{gff3,fasta,json}"
   - error_log:
-      type: file
-      description: Integrity error log if it failed
-      pattern: "integrity.out"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing meta information
+            e.g. `[ id:'accession1' ]`
+      - integrity_file:
+          type: file
+          description:
+            Captures potential errors detected during the integrity check of
+            a manifest file (manifest.json).
+          pattern: "integrity.out"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "@ensembl-dev"
 maintainers:
diff --git a/modules/ensembl/manifest/maker/meta.yml b/modules/ensembl/manifest/maker/meta.yml
index 0f56d39..704557a 100644
--- a/modules/ensembl/manifest/maker/meta.yml
+++ b/modules/ensembl/manifest/maker/meta.yml
@@ -1,6 +1,7 @@
----
 name: "manifest_maker"
-description: Generate a manifest and validate its JSON schema using provided input files and metadata.
+description:
+  Generate a manifest and validate its JSON schema using provided input
+  files and metadata.
 keywords:
   - ensembl
   - genomics
@@ -11,40 +12,22 @@ tools:
   - "manifest_maker":
       description: "Nextflow modules for genomic data file manifest comparison/checking."
       homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
-      
+      license: ["Apache License version 2.0"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession01' ]`
-  - manifest_files:
-      type: file
-      description: Set of genomic data files
-      pattern: "*.{gff3,fasta,json}"
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing meta information
+          e.g. `[ accession:'accession01' ]`
+    - file_name: {}
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession1' ]`
-
-  - all_files:
-      type: file
-      description: All files used as entry
-      pattern: "*.{gff3,fasta,json}"
-  - error_log:
-      type: file
-      description: Integrity error log if it failed
-      pattern: "integrity.out"
   - versions:
-      type: file
-      description: File containing information on module software version
-      pattern: "versions.yml"
-
+      - versions.yml:
+          type: file
+          description: File containing information on module software version
+          pattern: "versions.yml"
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
+  - "ensembl-dev@ebi.ac.uk"

From b203bc1dfb4301e4e4b4a8f2e225c6a10f6c753e Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 13:12:16 +0000
Subject: [PATCH 11/26] add nf-core lint

---
 .github/workflows/linting.yaml | 153 +++++++++++++++++++++++++++++++++
 1 file changed, 153 insertions(+)
 create mode 100644 .github/workflows/linting.yaml

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
new file mode 100644
index 0000000..bf31a3f
--- /dev/null
+++ b/.github/workflows/linting.yaml
@@ -0,0 +1,153 @@
+name: Run Linting
+on: [push, pull_request]
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VER: "25.10.2"
+  NXF_SYNTAX_PARSER: "v2"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  nf-core-changes:
+    name: nf-core-changes
+    runs-on:
+      - runs-on=${{ github.run_id }}-nf-core-changes
+      - runner=4cpu-linux-x64
+      - image=ubuntu22-full-x64
+    outputs:
+      modules: ${{ steps.filter.outputs.modules }}
+      modules_files: ${{ steps.module_names.outputs.result }}
+      subworkflows: ${{ steps.filter.outputs.subworkflows }}
+      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
+
+      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
+        id: filter
+        with:
+          filters: |
+            modules:
+              - added|modified: 'modules/ensembl/**'
+            subworkflows:
+              - added|modified: 'subworkflows/ensembl/**'
+          token: ""
+          list-files: "json"
+
+      - name: Get module name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.modules_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('modules/ensembl/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+      - name: Get subworkflow name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: subworkflow_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('subworkflows/ensembl/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+            
+  nf-core-lint-modules:
+    runs-on:
+      - runs-on=${{ github.run_id }}-nf-core-lint-modules
+      - runner=4cpu-linux-x64
+      - image=ubuntu22-full-x64
+    name: nf-core lint modules
+    needs: nf-core-changes
+    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5
+        id: cache-pip
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: |
+            ${{ runner.os }}-pip
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint module ${{ matrix.module }}
+        run: nf-core modules lint ${{ matrix.module }}
+
+  nf-core-lint-subworkflows:
+    runs-on:
+      - runs-on=${{ github.run_id }}-nf-core-lint-subworkflows
+      - runner=4cpu-linux-x64
+      - image=ubuntu22-full-x64
+    name: nf-core lint subworkflows
+    needs: nf-core-changes
+    if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }}
+    steps:
+      - name: Clean workspace
+        run: |
+          sudo rm -rf ./* || true
+          sudo rm -rf ./.* || true
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        with:
+          python-version: "3.14"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint subworkflow ${{ matrix.subworkflow }}
+        run: nf-core subworkflows lint ${{ matrix.subworkflow }}
\ No newline at end of file

From e5778facdc1a375c77ff651e03a10922cf8f1bc3 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 13:19:03 +0000
Subject: [PATCH 12/26] remove clean up

---
 .github/workflows/linting.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index bf31a3f..4d239d8 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -85,11 +85,6 @@ jobs:
       matrix:
         module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
     steps:
-      - name: Clean workspace
-        run: |
-          sudo rm -rf ./* || true
-          sudo rm -rf ./.* || true
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
       - name: Set up Python
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
@@ -133,11 +128,6 @@ jobs:
       matrix:
         subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }}
     steps:
-      - name: Clean workspace
-        run: |
-          sudo rm -rf ./* || true
-          sudo rm -rf ./.* || true
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
       - name: Set up Python
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:

From 96f8ac0709251adfffb1523f07510565ec357a34 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 13:54:19 +0000
Subject: [PATCH 13/26] clean up

---
 .github/workflows/linting.yaml | 82 +++-------------------------------
 1 file changed, 6 insertions(+), 76 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 4d239d8..eea87a7 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -5,7 +5,6 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
   NXF_VER: "25.10.2"
   NXF_SYNTAX_PARSER: "v2"
 
@@ -27,15 +26,6 @@ jobs:
       subworkflows: ${{ steps.filter.outputs.subworkflows }}
       subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
     steps:
-      - name: Clean workspace
-        run: |
-          sudo rm -rf ./* || true
-          sudo rm -rf ./.* || true
-
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-        with:
-          fetch-depth: 2 # To retrieve the preceding commit.
-
       - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
         id: filter
         with:
@@ -45,39 +35,11 @@ jobs:
             subworkflows:
               - added|modified: 'subworkflows/ensembl/**'
           token: ""
-          list-files: "json"
-
-      - name: Get module name
-        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
-        id: module_names
-        with:
-          script: |
-            return [...new Set(${{ steps.filter.outputs.modules_files }}
-              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
-              .map(path => path
-                .replace('modules/ensembl/', '')
-                .replace(/\/(main\.nf|tests\/.*)$/, '')
-              )
-            )];
-      - name: Get subworkflow name
-        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
-        id: subworkflow_names
-        with:
-          script: |
-            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
-              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
-              .map(path => path
-                .replace('subworkflows/ensembl/', '')
-                .replace(/\/(main\.nf|tests\/.*)$/, '')
-              )
-            )];
-            
-  nf-core-lint-modules:
-    runs-on:
-      - runs-on=${{ github.run_id }}-nf-core-lint-modules
-      - runner=4cpu-linux-x64
-      - image=ubuntu22-full-x64
-    name: nf-core lint modules
+          list-files: "json"         
+  
+  nf-core-lint:
+    runs-on: ubuntu-latest
+    name: nf-core-lint
     needs: nf-core-changes
     if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
     strategy:
@@ -101,43 +63,11 @@ jobs:
       - name: Install pip
         run: python -m pip install --upgrade pip
 
-      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
       - name: Lint module ${{ matrix.module }}
         run: nf-core modules lint ${{ matrix.module }}
-
-  nf-core-lint-subworkflows:
-    runs-on:
-      - runs-on=${{ github.run_id }}-nf-core-lint-subworkflows
-      - runner=4cpu-linux-x64
-      - image=ubuntu22-full-x64
-    name: nf-core lint subworkflows
-    needs: nf-core-changes
-    if: ${{ needs.nf-core-changes.outputs.subworkflows_files != '[]' }}
-    strategy:
-      fail-fast: false
-      matrix:
-        subworkflow: ${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files || '[]') }}
-    steps:
-      - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
-        with:
-          python-version: "3.14"
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
+  
       - name: Lint subworkflow ${{ matrix.subworkflow }}
         run: nf-core subworkflows lint ${{ matrix.subworkflow }}
\ No newline at end of file

From 24fd16fc5a831a58e99daa71fb721f932b313d7a Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 14:13:21 +0000
Subject: [PATCH 14/26] simplify linting

---
 .github/workflows/linting.yaml | 64 +++++++++++++++-------------------
 1 file changed, 28 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index eea87a7..802c528 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -1,4 +1,5 @@
 name: Run Linting
+
 on: [push, pull_request]
 
 env:
@@ -8,66 +9,57 @@ env:
   NXF_VER: "25.10.2"
   NXF_SYNTAX_PARSER: "v2"
 
-# Cancel if a newer run is started
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
   nf-core-changes:
-    name: nf-core-changes
-    runs-on:
-      - runs-on=${{ github.run_id }}-nf-core-changes
-      - runner=4cpu-linux-x64
-      - image=ubuntu22-full-x64
+    name: Detect changes
+    runs-on: ubuntu-latest
+
     outputs:
       modules: ${{ steps.filter.outputs.modules }}
-      modules_files: ${{ steps.module_names.outputs.result }}
       subworkflows: ${{ steps.filter.outputs.subworkflows }}
-      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
+
     steps:
-      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
+      - uses: actions/checkout@v6
+
+      - uses: dorny/paths-filter@v3
         id: filter
         with:
           filters: |
             modules:
-              - added|modified: 'modules/ensembl/**'
+              - 'modules/ensembl/**'
             subworkflows:
-              - added|modified: 'subworkflows/ensembl/**'
-          token: ""
-          list-files: "json"         
-  
+              - 'subworkflows/ensembl/**'
+
   nf-core-lint:
+    name: nf-core lint
     runs-on: ubuntu-latest
-    name: nf-core-lint
     needs: nf-core-changes
-    if: ${{ needs.nf-core-changes.outputs.modules_files != '[]' }}
-    strategy:
-      fail-fast: false
-      matrix:
-        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files || '[]') }}
+
     steps:
-      - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
         with:
-          python-version: "3.14"
+          python-version: "3.12"
 
-      - uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5
-        id: cache-pip
+      - uses: actions/cache@v5
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip
-          restore-keys: |
-            ${{ runner.os }}-pip
 
-      - name: Install pip
-        run: python -m pip install --upgrade pip
+      - uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools
+        run: pip install --upgrade git+https://github.com/nf-core/tools.git@dev
 
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
+      - name: Lint modules
+        if: needs.nf-core-changes.outputs.modules == 'true'
+        run: nf-core modules lint
 
-      - name: Lint module ${{ matrix.module }}
-        run: nf-core modules lint ${{ matrix.module }}
-  
-      - name: Lint subworkflow ${{ matrix.subworkflow }}
-        run: nf-core subworkflows lint ${{ matrix.subworkflow }}
\ No newline at end of file
+      - name: Lint subworkflows
+        if: needs.nf-core-changes.outputs.subworkflows == 'true'
+        run: nf-core subworkflows lint
\ No newline at end of file

From e319d8511240cab48043bc40abbfe7bb6f080699 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 14:22:55 +0000
Subject: [PATCH 15/26] add module names

---
 .github/workflows/linting.yaml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 802c528..8275bc9 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -38,7 +38,10 @@ jobs:
     name: nf-core lint
     runs-on: ubuntu-latest
     needs: nf-core-changes
-
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
     steps:
       - uses: actions/checkout@v6
 
@@ -58,8 +61,8 @@ jobs:
 
       - name: Lint modules
         if: needs.nf-core-changes.outputs.modules == 'true'
-        run: nf-core modules lint
+        run: nf-core modules lint ${{ matrix.tags }}
 
       - name: Lint subworkflows
         if: needs.nf-core-changes.outputs.subworkflows == 'true'
-        run: nf-core subworkflows lint
\ No newline at end of file
+        run: nf-core subworkflows lint --all 
\ No newline at end of file

From c9081efeb3a54b32a4c09222e887469ebb41a8ee Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 15:27:10 +0000
Subject: [PATCH 16/26] dont run if there is no changes

---
 .github/workflows/linting.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 8275bc9..bd66c2a 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -1,5 +1,4 @@
 name: Run Linting
-
 on: [push, pull_request]
 
 env:
@@ -7,7 +6,6 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   NXF_VER: "25.10.2"
-  NXF_SYNTAX_PARSER: "v2"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
@@ -38,6 +36,7 @@ jobs:
     name: nf-core lint
     runs-on: ubuntu-latest
     needs: nf-core-changes
+    if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
@@ -60,7 +59,6 @@ jobs:
         run: pip install --upgrade git+https://github.com/nf-core/tools.git@dev
 
       - name: Lint modules
-        if: needs.nf-core-changes.outputs.modules == 'true'
         run: nf-core modules lint ${{ matrix.tags }}
 
       - name: Lint subworkflows

From e15843f7d51935441bbd367c67a72cf62604d2bb Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 15:38:47 +0000
Subject: [PATCH 17/26] correcting the id

---
 .github/workflows/linting.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index bd66c2a..f5cfe83 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -36,11 +36,11 @@ jobs:
     name: nf-core lint
     runs-on: ubuntu-latest
     needs: nf-core-changes
-    if: needs.changes.outputs.modules != '[]'
+    if: needs.nf-core-changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        tags: ["${{ fromJson(needs.nf-core-changes.outputs.modules) }}"]
     steps:
       - uses: actions/checkout@v6
 

From 7533b612251e4e57097b4ac0614fdea0841c07d7 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Mon, 16 Mar 2026 17:14:21 +0000
Subject: [PATCH 18/26] correcting modules list

---
 .github/workflows/linting.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index f5cfe83..2c2eadc 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -31,6 +31,7 @@ jobs:
               - 'modules/ensembl/**'
             subworkflows:
               - 'subworkflows/ensembl/**'
+          list-files: "json"
 
   nf-core-lint:
     name: nf-core lint
@@ -46,7 +47,7 @@ jobs:
 
       - uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.14"
 
       - uses: actions/cache@v5
         with:
@@ -63,4 +64,4 @@ jobs:
 
       - name: Lint subworkflows
         if: needs.nf-core-changes.outputs.subworkflows == 'true'
-        run: nf-core subworkflows lint --all 
\ No newline at end of file
+        run: nf-core subworkflows lint --all
\ No newline at end of file

From a5a9800f99be1c28253ae5fc301bde8d4221e068 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 13:38:22 +0000
Subject: [PATCH 19/26] trying to extract module names for lint

---
 .github/workflows/linting.yaml | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 2c2eadc..d50e90a 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -17,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      modules: ${{ steps.filter.outputs.modules }}
-      subworkflows: ${{ steps.filter.outputs.subworkflows }}
-
+      modules: ${{ steps.filter.outputs.modules_files }}
+      subworkflows: ${{ steps.filter.outputs.subworkflows_files }}
+    
     steps:
       - uses: actions/checkout@v6
 
@@ -32,6 +32,19 @@ jobs:
             subworkflows:
               - 'subworkflows/ensembl/**'
           list-files: "json"
+          
+      - name: Extract module names
+        id: modules
+        run: |
+          echo '${{ steps.filter.outputs.modules_files }}' \
+          | jq -r 'map(split("/")[2]) | unique' \
+          > modules.json
+          echo "modules=$(cat modules.json)" >> $GITHUB_OUTPUT
+      
+      - name: Debug
+        run: |
+          echo "RAW: ${{ steps.filter.outputs.modules }}"
+          echo "FILES: ${{ steps.filter.outputs.modules_files }}"
 
   nf-core-lint:
     name: nf-core lint
@@ -41,7 +54,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        tags: ["${{ fromJson(needs.nf-core-changes.outputs.modules) }}"]
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules || '[]') }}
     steps:
       - uses: actions/checkout@v6
 
@@ -60,7 +73,7 @@ jobs:
         run: pip install --upgrade git+https://github.com/nf-core/tools.git@dev
 
       - name: Lint modules
-        run: nf-core modules lint ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.module }}
 
       - name: Lint subworkflows
         if: needs.nf-core-changes.outputs.subworkflows == 'true'

From c206dda8979973b186388c5fe0c41807cdbaef77 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 13:53:24 +0000
Subject: [PATCH 20/26] linting extracting the correct module

---
 .github/workflows/linting.yaml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index d50e90a..81777e2 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -37,14 +37,9 @@ jobs:
         id: modules
         run: |
           echo '${{ steps.filter.outputs.modules_files }}' \
-          | jq -r 'map(split("/")[2]) | unique' \
+          | jq -r 'map((split("/")[2] + "/" + split("/")[3])) | unique' \
           > modules.json
           echo "modules=$(cat modules.json)" >> $GITHUB_OUTPUT
-      
-      - name: Debug
-        run: |
-          echo "RAW: ${{ steps.filter.outputs.modules }}"
-          echo "FILES: ${{ steps.filter.outputs.modules_files }}"
 
   nf-core-lint:
     name: nf-core lint

From 790a0352959ead6523d28da3bbb0085b4908cae7 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 14:17:09 +0000
Subject: [PATCH 21/26] linting extracting the correct module

---
 .github/workflows/linting.yaml | 54 ++++++++++++++++++++++++----------
 1 file changed, 39 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 81777e2..28156e8 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -17,29 +17,53 @@ jobs:
     runs-on: ubuntu-latest
 
     outputs:
-      modules: ${{ steps.filter.outputs.modules_files }}
-      subworkflows: ${{ steps.filter.outputs.subworkflows_files }}
-    
+      # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files
+      modules: ${{ steps.filter.outputs.modules }}
+      modules_files: ${{ steps.module_names.outputs.result }}
+      subworkflows: ${{ steps.filter.outputs.subworkflows }}
+      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
     steps:
-      - uses: actions/checkout@v6
-
-      - uses: dorny/paths-filter@v3
+      - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
         id: filter
         with:
           filters: |
             modules:
-              - 'modules/ensembl/**'
+              - added|modified: 'modules/ensembl/**'
             subworkflows:
-              - 'subworkflows/ensembl/**'
+              - added|modified: 'subworkflows/ensembl/**'
+          token: ""
           list-files: "json"
-          
-      - name: Extract module names
-        id: modules
+
+      - name: Get module name
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.modules_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('modules/ensembl/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+
+      - name: Get subworkflow name
+        id: subworkflow_names
+        with:
+          script: |
+            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
+              .filter(x => x.endsWith('main.nf') || x.endsWith('.nf.test.snap'))
+              .map(path => path
+                .replace('subworkflows/nf-core/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+
+      - name: debug
         run: |
-          echo '${{ steps.filter.outputs.modules_files }}' \
-          | jq -r 'map((split("/")[2] + "/" + split("/")[3])) | unique' \
-          > modules.json
-          echo "modules=$(cat modules.json)" >> $GITHUB_OUTPUT
+          echo ${{ steps.filter.outputs.modules_files }}
+          echo ${{ steps.module_names.outputs.result }}
+          echo ${{ steps.filter.outputs.subworkflows_files }}
+          echo ${{ steps.subworkflow_names.outputs.result }}
 
   nf-core-lint:
     name: nf-core lint

From dccbe8e89eb8eabfb5675607266140ef504c47e7 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 14:24:31 +0000
Subject: [PATCH 22/26] linting extracting the module nf-core style

---
 .github/workflows/linting.yaml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 28156e8..c60d12f 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -23,6 +23,7 @@ jobs:
       subworkflows: ${{ steps.filter.outputs.subworkflows }}
       subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
     steps:
+  
       - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
         id: filter
         with:
@@ -35,6 +36,7 @@ jobs:
           list-files: "json"
 
       - name: Get module name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
         id: module_names
         with:
           script: |
@@ -45,8 +47,8 @@ jobs:
                 .replace(/\/(main\.nf|tests\/.*)$/, '')
               )
             )];
-
       - name: Get subworkflow name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
         id: subworkflow_names
         with:
           script: |
@@ -65,15 +67,16 @@ jobs:
           echo ${{ steps.filter.outputs.subworkflows_files }}
           echo ${{ steps.subworkflow_names.outputs.result }}
 
+
   nf-core-lint:
     name: nf-core lint
     runs-on: ubuntu-latest
     needs: nf-core-changes
-    if: needs.nf-core-changes.outputs.modules != '[]'
+    if: needs.nf-core-changes.outputs.modules_files != '[]'
     strategy:
       fail-fast: false
       matrix:
-        module: ${{ fromJson(needs.nf-core-changes.outputs.modules || '[]') }}
+        module: ${{ fromJson(needs.nf-core-changes.outputs.modules_files) }}
     steps:
       - uses: actions/checkout@v6
 

From 576a2d34d111ce2518f78b5124e2eb2b0f76d221 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 14:28:27 +0000
Subject: [PATCH 23/26] actions update

---
 .github/workflows/linting.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index c60d12f..64576e1 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -23,7 +23,10 @@ jobs:
       subworkflows: ${{ steps.filter.outputs.subworkflows }}
       subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
     steps:
-  
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          
       - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
         id: filter
         with:

From fd4378d7f4f693370b3b059deb6b8e612c6ca36b Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 14:35:53 +0000
Subject: [PATCH 24/26] update snap

---
 .../urls/extract/tests/main.nf.test.snap      | 32 ++++++++---------
 .../urls/generate/tests/main.nf.test.snap     | 36 +++++++++----------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/modules/ensembl/urls/extract/tests/main.nf.test.snap b/modules/ensembl/urls/extract/tests/main.nf.test.snap
index fff3475..aa3b76d 100644
--- a/modules/ensembl/urls/extract/tests/main.nf.test.snap
+++ b/modules/ensembl/urls/extract/tests/main.nf.test.snap
@@ -14,11 +14,11 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:10:02.948488",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:02.948488"
+        }
     },
     "versions": {
         "content": [
@@ -26,11 +26,11 @@
                 "versions.yml:md5,844210d41d31414da2041f13946f845c"
             ]
         ],
+        "timestamp": "2025-03-26T15:10:02.953735",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:02.953735"
+        }
     },
     "versions_no_database": {
         "content": [
@@ -38,23 +38,23 @@
                 "versions.yml:md5,844210d41d31414da2041f13946f845c"
             ]
         ],
+        "timestamp": "2025-03-26T15:10:06.887747",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:06.887747"
+        }
     },
     "Should fail with invalid URL format": {
         "content": [
             [
-                "\u001b[33mNextflow 25.04.4 is available - Please consider updating your version to it\u001b(B\u001b[m"
+                "\u001b[33mNextflow 25.10.4 is available - Please consider updating your version to it\u001b(B\u001b[m"
             ]
         ],
+        "timestamp": "2026-03-17T14:33:46.160581013",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-06-17T11:30:46.552594268"
+        }
     },
     "versions_no_password": {
         "content": [
@@ -62,11 +62,11 @@
                 "versions.yml:md5,844210d41d31414da2041f13946f845c"
             ]
         ],
+        "timestamp": "2025-03-26T15:10:04.907779",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:04.907779"
+        }
     },
     "connection_info_no_password": {
         "content": [
@@ -83,11 +83,11 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:10:04.9047",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:04.9047"
+        }
     },
     "connection_info_no_database": {
         "content": [
@@ -104,10 +104,10 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:10:06.883916",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:10:06.883916"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/urls/generate/tests/main.nf.test.snap b/modules/ensembl/urls/generate/tests/main.nf.test.snap
index 376ccf6..9fb5ed0 100644
--- a/modules/ensembl/urls/generate/tests/main.nf.test.snap
+++ b/modules/ensembl/urls/generate/tests/main.nf.test.snap
@@ -2,38 +2,38 @@
     "versions_no_database": {
         "content": [
             [
-                "versions.yml:md5,d817b1f3c9f2bd1f04c668984320951c"
+                "versions.yml:md5,ac2fb3abdcb67053013a354749ce87f8"
             ]
         ],
+        "timestamp": "2026-03-17T14:34:20.337929175",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-06-17T11:31:22.822012541"
+        }
     },
     "versions_full": {
         "content": [
             [
-                "versions.yml:md5,d817b1f3c9f2bd1f04c668984320951c"
+                "versions.yml:md5,ac2fb3abdcb67053013a354749ce87f8"
             ]
         ],
+        "timestamp": "2026-03-17T14:33:57.911274653",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-06-17T11:30:59.208840884"
+        }
     },
     "versions_no_password": {
         "content": [
             [
-                "versions.yml:md5,d817b1f3c9f2bd1f04c668984320951c"
+                "versions.yml:md5,ac2fb3abdcb67053013a354749ce87f8"
             ]
         ],
+        "timestamp": "2026-03-17T14:34:09.150646453",
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.4",
             "nextflow": "24.10.3"
-        },
-        "timestamp": "2025-06-17T11:31:11.312214413"
+        }
     },
     "generated_url_full": {
         "content": [
@@ -46,11 +46,11 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:48:40.650816",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:48:40.650816"
+        }
     },
     "generated_url_no_password": {
         "content": [
@@ -63,11 +63,11 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:48:42.651032",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:48:42.651032"
+        }
     },
     "generated_url_no_database": {
         "content": [
@@ -80,10 +80,10 @@
                 ]
             ]
         ],
+        "timestamp": "2025-03-26T15:48:44.600396",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T15:48:44.600396"
+        }
     }
 }
\ No newline at end of file

From aabf62e3affb67dde9ed2fa5aa0bff2480d09596 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 15:47:08 +0000
Subject: [PATCH 25/26] correct nf-lint

---
 modules/ensembl/annotation/dumpanno/meta.yml  |  62 ++++++----
 modules/ensembl/database/dbfactory/meta.yml   |  55 +++++----
 .../ensembl/download/assemblydata/meta.yml    |  53 ++++----
 modules/ensembl/download/genbank/meta.yml     |  51 ++++----
 modules/ensembl/dump/genomestats/meta.yml     |  65 +++++-----
 modules/ensembl/fasta/dumpfastanuc/meta.yml   |  71 +++++------
 .../ensembl/fasta/dumpfastapeptide/meta.yml   |  71 +++++------
 modules/ensembl/genbank/extractgb/meta.yml    | 116 +++++++-----------
 modules/ensembl/gff3/dumpgff3/meta.yml        |  73 +++++------
 modules/ensembl/gff3/validation/meta.yml      |  65 +++++-----
 modules/ensembl/manifest/integrity/meta.yml   |  83 +++++++------
 modules/ensembl/manifest/maker/meta.yml       |  39 +++---
 modules/ensembl/metadata/amendgenome/meta.yml |  89 +++++++-------
 .../ensembl/metadata/genomesummary/meta.yml   |  72 ++++++-----
 modules/ensembl/schema/json/meta.yml          |  48 ++++++++
 15 files changed, 526 insertions(+), 487 deletions(-)
 create mode 100644 modules/ensembl/schema/json/meta.yml

diff --git a/modules/ensembl/annotation/dumpanno/meta.yml b/modules/ensembl/annotation/dumpanno/meta.yml
index 8d6bd20..4656902 100644
--- a/modules/ensembl/annotation/dumpanno/meta.yml
+++ b/modules/ensembl/annotation/dumpanno/meta.yml
@@ -1,39 +1,47 @@
-name: "annotation_dumpanno"
-
-description:
-  This module is used to dump the functional annotation of a genome from
-  core databases.
+---
+name: "database_dbfactory"
+description: >
+  Generate a list of one or more databases plus some associated meta table information.
 
 keywords:
   - container
   - core_database
   - docker
-  - ensembl-legacy-scripts
-  - fasta
+  - database
+  - ensembl-genomio
 
 tools:
-  - "annotation":
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      description:
-        "This module handles all annotation-related interactions with the\
-        \ core database, including annotation dumping and processing"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  database:
+    description: >
+      Modules which function to read or write information from core databases.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  # Only when we have meta
-  - - db: {}
+  - name: server
+    type: map
+    description: >
+      Groovy Map containing MySQL server host, port, user, and password meta information,
+      e.g. `[ host:"mysql-host-test-prod" ]`
+
+  - name: filter_map
+    type: file
+    description: "JSON file containing database filter information."
+    pattern: "*.json"
+
 output:
-  - functional_annotation:
-      - db: {}
-      - functional_annotation: {}
-      - "*.json": {}
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions.
-          pattern: "versions.yml"
+  - name: dbs_meta
+    type: file
+    description: "JSON file containing database metadata."
+    pattern: "dbs.json"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
-  - "@ensembl-dev"
+  - "ensembl-dev@ebi.ac.uk"
 maintainers:
-  - "@ensembl-dev"
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/database/dbfactory/meta.yml b/modules/ensembl/database/dbfactory/meta.yml
index 25f5444..4656902 100644
--- a/modules/ensembl/database/dbfactory/meta.yml
+++ b/modules/ensembl/database/dbfactory/meta.yml
@@ -1,7 +1,7 @@
+---
 name: "database_dbfactory"
-description:
-  Generate a list of one or more databases plus some associated meta table
-  information.
+description: >
+  Generate a list of one or more databases plus some associated meta table information.
 
 keywords:
   - container
@@ -11,31 +11,36 @@ keywords:
   - ensembl-genomio
 
 tools:
-  - database:
-      description: "Modules which function to read or write information from core databases."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  database:
+    description: >
+      Modules which function to read or write information from core databases.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - server:
-        type: map
-        description: >
-          Groovy Map containing mysql server host, port, user and password meta  and
-          file of JSON database filter information.
-          e.g. [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
-    - filter_map: {}
+  - name: server
+    type: map
+    description: >
+      Groovy Map containing MySQL server host, port, user, and password meta information,
+      e.g. `[ host:"mysql-host-test-prod" ]`
+
+  - name: filter_map
+    type: file
+    description: "JSON file containing database filter information."
+    pattern: "*.json"
+
 output:
-  - dbs_meta_json:
-      - dbs.json:
-          type: file
-          description: "JSON file containing database metadata."
-          pattern: "dbs.json"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: dbs_meta
+    type: file
+    description: "JSON file containing database metadata."
+    pattern: "dbs.json"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/download/assemblydata/meta.yml b/modules/ensembl/download/assemblydata/meta.yml
index 63372ea..16e2c39 100644
--- a/modules/ensembl/download/assemblydata/meta.yml
+++ b/modules/ensembl/download/assemblydata/meta.yml
@@ -1,7 +1,7 @@
+---
 name: "download_assemblydata"
-description:
-  Generate a list of one or more databases plus some associated meta table
-  information.
+description: >
+  Generate a list of one or more databases plus some associated meta table information.
 
 keywords:
   - ensembl-genomio
@@ -13,28 +13,37 @@ keywords:
   - INSDC
 
 tools:
-  - download:
-      description:
-        "Modules which function to download information or various data from\
-        \ externally hosted resources."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  download:
+    description: >
+      Modules which function to download information or various data from
+      externally hosted resources.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing A single INSDC GCA or NCBI 'amended' GCF genome assembly accession meta information.
-          e.g. `[ accession:'GCA_000000000.1' ]`
+  - name: meta
+    type: map
+    description: >
+      Groovy Map containing a single INSDC GCA or NCBI 'amended' GCF genome assembly accession meta information,
+      e.g. `[ accession:'GCA_000000000.1' ]`
+
 output:
-  - min_set: []
-  - opt_set: []
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: min_set
+    type: file
+    description: "Minimal set of downloaded assembly data files"
+    pattern: "*"
+
+  - name: opt_set
+    type: file
+    description: "Optional set of downloaded assembly data files"
+    pattern: "*"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/download/genbank/meta.yml b/modules/ensembl/download/genbank/meta.yml
index 151d5b9..153b23a 100644
--- a/modules/ensembl/download/genbank/meta.yml
+++ b/modules/ensembl/download/genbank/meta.yml
@@ -1,5 +1,7 @@
+---
 name: "download_genbank"
-description: Download a single sequence from NCBI GenBank.
+description: >
+  Download a single sequence from NCBI GenBank.
 
 keywords:
   - core_database
@@ -10,31 +12,34 @@ keywords:
   - genomics
 
 tools:
-  - download:
-      description:
-        "Modules which function to download information or various data from\
-        \ externally hosted resources."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  download:
+    description: >
+      Modules which function to download information or various data from
+      externally hosted resources.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - meta: {}
+  - name: meta
+    type: map
+    description: "Optional meta information about the sequence to download."
+
 output:
-  - gb_sequence:
-      - meta:
-          type: file
-          description: A sequence record outfile in genbank format.
-          pattern: "output.gb"
-      - output.gb:
-          type: file
-          description: A sequence record outfile in genbank format.
-          pattern: "output.gb"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: gb_sequence_file
+    type: file
+    description: "A sequence record outfile in GenBank format"
+    pattern: "output.gb"
+
+  - name: gb_sequence_meta
+    type: map
+    description: "Metadata associated with the downloaded GenBank sequence"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/dump/genomestats/meta.yml b/modules/ensembl/dump/genomestats/meta.yml
index 1e69215..80d5967 100644
--- a/modules/ensembl/dump/genomestats/meta.yml
+++ b/modules/ensembl/dump/genomestats/meta.yml
@@ -1,5 +1,8 @@
+---
 name: "dump_genomestats"
-description: A module for dumping a core database
+description: >
+  A module for dumping a core database, including assembly and annotation statistics.
+
 keywords:
   - container
   - core_database
@@ -8,41 +11,37 @@ keywords:
   - json
 
 tools:
-  - dump:
-      description:
-        "Modules which function to dump various forms of data from a core\
-        \ database."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  dump:
+    description: >
+      Modules which function to dump various forms of data from a core database.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - db:
-        type: map
-        description: >
-          A meta map including 'core database name'.
-          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
-          ...]]
-          pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+  - name: db
+    type: map
+    description: >
+      A meta map including 'core database name',
+      e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
+    pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+
 output:
-  - core_stats:
-      - db:
-          type: map
-          description: >
-            JSON file containing core database statistics (assembly and annotation).
-            e.g [ db:"database name", file("core_stats.json") ]
-            pattern: "core_stats.json"
-      - core_stats.json:
-          type: map
-          description: >
-            JSON file containing core database statistics (assembly and annotation).
-            e.g [ db:"database name", file("core_stats.json") ]
-            pattern: "core_stats.json"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: core_stats_meta
+    type: map
+    description: >
+      Metadata for the core database statistics JSON, e.g. [ db:"database name", file("core_stats.json") ]
+
+  - name: core_stats_file
+    type: file
+    description: "JSON file containing core database statistics (assembly and annotation)"
+    pattern: "core_stats.json"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/fasta/dumpfastanuc/meta.yml b/modules/ensembl/fasta/dumpfastanuc/meta.yml
index 0b6c504..3ceff2b 100644
--- a/modules/ensembl/fasta/dumpfastanuc/meta.yml
+++ b/modules/ensembl/fasta/dumpfastanuc/meta.yml
@@ -1,5 +1,7 @@
+---
 name: "fasta_dumpfastanuc"
-description: A module for dumping core database gene module nucleotide fasta seqs
+description: >
+  A module for dumping core database gene module nucleotide FASTA sequences.
 
 keywords:
   - container
@@ -10,47 +12,38 @@ keywords:
   - fasta
 
 tools:
-  - "fasta":
-      description:
-        "Modules which function to facilitate data deposition/retrieval of\
-        \ fasta sequences."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  fasta:
+    description: >
+      Modules which function to facilitate data deposition and retrieval
+      of FASTA sequences.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - db:
-        type: map
-        description: >
-          A meta map including 'core database name'.
-          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
-          ...]]
-        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+  - name: db
+    type: map
+    description: >
+      A meta map including 'core database name',
+      e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
+    pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+
 output:
-  - nucleotide_fasta:
-      - db:
-          type: map
-          description: >
-            Fasta file containing nucleotide sequence(s).
-            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
-          pattern: "*_fasta_dna.fasta"
-      - fasta_dna:
-          type: map
-          description: >
-            Fasta file containing nucleotide sequence(s).
-            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
-          pattern: "*_fasta_dna.fasta"
-      - "*.fasta":
-          type: map
-          description: >
-            Fasta file containing nucleotide sequence(s).
-            e.g [ db:'database name', file("*_fasta_dna.fasta") ]
-          pattern: "*_fasta_dna.fasta"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: nucleotide_fasta_meta
+    type: map
+    description: >
+      Metadata for nucleotide FASTA sequences, e.g. [ db:'database name', file("*_fasta_dna.fasta") ]
+
+  - name: nucleotide_fasta_file
+    type: file
+    description: "Nucleotide FASTA sequences from the database"
+    pattern: "*_fasta_dna.fasta"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/fasta/dumpfastapeptide/meta.yml b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
index 3a02fcb..c6feafd 100644
--- a/modules/ensembl/fasta/dumpfastapeptide/meta.yml
+++ b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
@@ -1,5 +1,7 @@
+---
 name: "fasta_dumpfastapeptide"
-description: A module for dumping peptide FASTA sequences from core databases
+description: >
+  A module for dumping peptide FASTA sequences from core databases.
 
 keywords:
   - container
@@ -10,47 +12,38 @@ keywords:
   - fasta
 
 tools:
-  - "fasta":
-      description:
-        "Modules which function to facilitate data deposition/retrieval of\
-        \ fasta sequences."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  fasta:
+    description: >
+      Modules which function to facilitate data deposition and retrieval
+      of FASTA sequences.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - db:
-        type: map
-        description: >
-          A meta map including 'core database name'.
-          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
-          ...]]
-        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+  - name: db
+    type: map
+    description: >
+      A meta map including 'core database name',
+      e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
+    pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+
 output:
-  - peptide_fasta:
-      - db:
-          type: map
-          description: >
-            Fasta file containing peptide sequence(s).
-            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
-          pattern: "*_fasta_pep.fasta"
-      - fasta_pep:
-          type: map
-          description: >
-            Fasta file containing peptide sequence(s).
-            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
-          pattern: "*_fasta_pep.fasta"
-      - "*.fasta":
-          type: map
-          description: >
-            Fasta file containing peptide sequence(s).
-            e.g [ db:'database name', file("*_fasta_pep.fasta") ]
-          pattern: "*_fasta_pep.fasta"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: peptide_fasta_meta
+    type: map
+    description: >
+      Metadata for peptide FASTA sequences, e.g. [ db:'database name', file("*_fasta_pep.fasta") ]
+
+  - name: peptide_fasta_file
+    type: file
+    description: "Peptide FASTA sequences from the database"
+    pattern: "*_fasta_pep.fasta"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/genbank/extractgb/meta.yml b/modules/ensembl/genbank/extractgb/meta.yml
index 172113b..fd4d090 100644
--- a/modules/ensembl/genbank/extractgb/meta.yml
+++ b/modules/ensembl/genbank/extractgb/meta.yml
@@ -1,6 +1,7 @@
+---
 name: "genbank_extractgb"
-description:
-  Parse a GenBank file and create cleaned up files and validate generated
+description: >
+  Parse a GenBank file and create cleaned up files, validating generated
   JSON files.
 
 keywords:
@@ -12,76 +13,53 @@ keywords:
   - genomics
 
 tools:
-  - "genbank":
-      description:
-        "Modules with functions related to work with Genbank related data\
-        \ files."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  genbank:
+    description: >
+      Modules with functions related to working with GenBank data files.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing genome database meta information
-          e.g. `[ accession:'NC_XXXX.X' ]`
-    - gb_file:
-        type: file
-        description: |
-          File path to genbank formatted input file (*.gb)
-          e.g. `[gb_file("genome.gb")]`
+  - name: meta
+    type: map
+    description: "Groovy Map containing genome database meta information, e.g. `[ accession:'NC_XXXX.X' ]`"
+
+  - name: gb_file
+    type: file
+    description: "File path to GenBank formatted input file (*.gb), e.g. `[gb_file('genome.gb')]`"
+
 output:
-  - genome:
-      - meta:
-          type: file
-          description: Genome metadata (JSON)
-          pattern: "genome.json"
-      - genome.json:
-          type: file
-          description: Genome metadata (JSON)
-          pattern: "genome.json"
-  - seq_regions:
-      - meta:
-          type: file
-          description: Sequence region(s) meta (JSON)
-          pattern: "seq_region.json"
-      - seq_region.json:
-          type: file
-          description: Sequence region(s) meta (JSON)
-          pattern: "seq_region.json"
-  - dna_fasta:
-      - meta:
-          type: file
-          description: Genome nucleotide sequence(s) (FASTA)
-          pattern: "dna.fasta"
-      - dna.fasta:
-          type: file
-          description: Genome nucleotide sequence(s) (FASTA)
-          pattern: "dna.fasta"
-  - gene_gff:
-      - meta:
-          type: file
-          description: Gene model information (GFF3)
-          pattern: "*.gff"
-      - "*.gff":
-          type: file
-          description: Gene model information (GFF3)
-          pattern: "*.gff"
-  - pep_fasta:
-      - meta:
-          type: file
-          description: Genome protein-coding gene amino acid sequence(s) (FASTA)
-          pattern: "pep.fasta"
-      - pep.fasta:
-          type: file
-          description: Genome protein-coding gene amino acid sequence(s) (FASTA)
-          pattern: "pep.fasta"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: genome_meta
+    type: file
+    description: "Genome metadata (JSON)"
+    pattern: "genome.json"
+
+  - name: seq_regions_meta
+    type: file
+    description: "Sequence region(s) metadata (JSON)"
+    pattern: "seq_region.json"
+
+  - name: dna_fasta
+    type: file
+    description: "Genome nucleotide sequence(s) (FASTA)"
+    pattern: "dna.fasta"
+
+  - name: gene_gff
+    type: file
+    description: "Gene model information (GFF3)"
+    pattern: "*.gff"
+
+  - name: pep_fasta
+    type: file
+    description: "Genome protein-coding gene amino acid sequence(s) (FASTA)"
+    pattern: "pep.fasta"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/gff3/dumpgff3/meta.yml b/modules/ensembl/gff3/dumpgff3/meta.yml
index 2df6712..2aa4365 100644
--- a/modules/ensembl/gff3/dumpgff3/meta.yml
+++ b/modules/ensembl/gff3/dumpgff3/meta.yml
@@ -1,5 +1,8 @@
+---
 name: "gff3_dumpgff3"
-description: write your description here
+description: >
+  Dump GFF3 gene models from a core Ensembl database into GFF3 files.
+  (Add more details as needed.)
 
 keywords:
   - container
@@ -9,47 +12,39 @@ keywords:
   - gff3
 
 tools:
-  - "gff3":
-      description:
-        "Modules for GFF3 validation, data deposition and retrieval from/into\
-        \ GFF3 file format"
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  gff3:
+    description: >
+      Modules for GFF3 validation, data deposition, and retrieval from/into
+      GFF3 file format.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - db:
-        type: map
-        description: >
-          A meta map including 'core database name'.
-          e.g. [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species',
-          ...]]
-        pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+  - name: db
+    type: map
+    description: >
+      A meta map including 'core database name', e.g.
+      [[ db:'genus_species_gca00000000v1_core_110_1', species:'Genus species', ...]]
+    pattern: "[a-z]+_[a-z]_gc[af][0-9]v[0-9]+_core_*"
+
 output:
-  - gff3:
-      - db:
-          type: map
-          description: >
-            GFF3 file containing gene model(s).
-            e.g [ db:'database name', file("*.gff3") ]
-          pattern: "*.gff3"
-      - gff3:
-          type: map
-          description: >
-            GFF3 file containing gene model(s).
-            e.g [ db:'database name', file("*.gff3") ]
-          pattern: "*.gff3"
-      - "*.gff3":
-          type: map
-          description: >
-            GFF3 file containing gene model(s).
-            e.g [ db:'database name', file("*.gff3") ]
-          pattern: "*.gff3"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: gff3_meta
+    type: map
+    description: >
+      GFF3 file metadata including database information, e.g.
+      [ db:'database name', file("*.gff3") ]
+
+  - name: gff3_file
+    type: file
+    description: "GFF3 file containing gene model(s)."
+    pattern: "*.gff3"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version."
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/gff3/validation/meta.yml b/modules/ensembl/gff3/validation/meta.yml
index 0a18747..e7d8784 100644
--- a/modules/ensembl/gff3/validation/meta.yml
+++ b/modules/ensembl/gff3/validation/meta.yml
@@ -1,5 +1,7 @@
+---
 name: "gff3_validation"
-description: Check for proper validation of the GFF3 using GenomeTools.
+description: >
+  Check for proper validation of GFF3 files using GenomeTools.
 
 keywords:
   - ensembl
@@ -10,40 +12,39 @@ keywords:
   - validation
 
 tools:
-  - "gff3":
-      description:
-        "Modules for GFF3 validation, data deposition and retrieval from/into\
-        \ GFF3 file format"
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  gff3:
+    description: >
+      Modules for GFF3 validation, data deposition, and retrieval from/into
+      GFF3 file format.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing meta information
-          e.g. `[ id:'accession1' ]`
-    - gene_models:
-        type: file
-        description: GFF3 files
-        pattern: "*.{gff3}"
+  - name: meta
+    type: map
+    description: "Groovy Map containing meta information, e.g. `[ id:'accession1' ]`"
+
+  - name: gene_models
+    type: file
+    description: "GFF3 files"
+    pattern: "*.{gff3}"
+
 output:
-  - gene_models:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing meta information
-            e.g. `[ id:'accession1' ]`
-      - gene_models.gff3:
-          type: file
-          description: All files used as entry
-          pattern: "*.{gff3}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: gene_models_meta
+    type: map
+    description: "Groovy Map containing meta information, e.g. `[ id:'accession1' ]`"
+
+  - name: gene_models_file
+    type: file
+    description: "All GFF3 files used as input"
+    pattern: "*.{gff3}"
+
+  - name: versions
+    type: file
+    description: "File containing information on module software version"
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/manifest/integrity/meta.yml b/modules/ensembl/manifest/integrity/meta.yml
index 0f4df00..d18bfcf 100644
--- a/modules/ensembl/manifest/integrity/meta.yml
+++ b/modules/ensembl/manifest/integrity/meta.yml
@@ -1,5 +1,7 @@
+---
 name: "manifest_integrity"
-description: Check the data integrity of a set of genomic files, listed by their manifest.
+description: >
+  Check the data integrity of a set of genomic files, listed by their manifest.
 keywords:
   - ensembl
   - genomics
@@ -8,50 +10,47 @@ keywords:
   - validation
 
 tools:
-  - "manifest":
-      description: "Nextflow modules for genomic data file manifest comparison/checking"
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  manifest:
+    description: "Nextflow modules for genomic data file manifest comparison/checking"
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing meta information
-          e.g. `[ id:'accession1' ]`
-    - manifest_files:
-        type: file
-        description: Set of genomic data files
-        pattern: "*.{gff3,fasta,json}"
+  - name: meta
+    type: map
+    description: "Groovy Map containing meta information, e.g. `[ id:'accession1' ]`"
+
+  - name: manifest_files
+    type: file
+    description: "Set of genomic data files"
+    pattern: "*.{gff3,fasta,json}"
+
 output:
-  - all_files:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing meta information
-            e.g. `[ id:'accession1' ]`
-      - '*.*", includeInputs: true':
-          type: file
-          description: All files used as entry.
-          pattern: "*.{gff3,fasta,json}"
-  - error_log:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing meta information
-            e.g. `[ id:'accession1' ]`
-      - integrity_file:
-          type: file
-          description:
-            Captures potential errors detected during the integrity check of
-            a manifest file (manifest.json).
-          pattern: "integrity.out"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: all_files_meta
+    type: map
+    description: "Groovy Map containing meta information, e.g. `[ id:'accession1' ]`"
+
+  - name: all_files
+    type: file
+    description: "All files used as entry"
+    pattern: "*.{gff3,fasta,json}"
+    includeInputs: true
+
+  - name: error_log_meta
+    type: map
+    description: "Groovy Map containing meta information, e.g. `[ id:'accession1' ]`"
+
+  - name: integrity_file
+    type: file
+    description: "Captures potential errors detected during integrity check"
+    pattern: "integrity.out"
+
+  - name: versions
+    type: file
+    description: "File containing module software versions"
+    pattern: "versions.yml"
+
 authors:
   - "@ensembl-dev"
 maintainers:
diff --git a/modules/ensembl/manifest/maker/meta.yml b/modules/ensembl/manifest/maker/meta.yml
index 704557a..1c3dece 100644
--- a/modules/ensembl/manifest/maker/meta.yml
+++ b/modules/ensembl/manifest/maker/meta.yml
@@ -1,5 +1,6 @@
+---
 name: "manifest_maker"
-description:
+description: >
   Generate a manifest and validate its JSON schema using provided input
   files and metadata.
 keywords:
@@ -8,25 +9,29 @@ keywords:
   - genomio
   - integrity
   - validation
+
 tools:
-  - "manifest_maker":
-      description: "Nextflow modules for genomic data file manifest comparison/checking."
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ["Apache License version 2.0"]
-      identifier: ""
+  manifest_maker:
+    description: "Nextflow modules for genomic data file manifest comparison/checking."
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
+
 input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing meta information
-          e.g. `[ accession:'accession01' ]`
-    - file_name: {}
+  - name: meta
+    type: map
+    description: >
+      Groovy Map containing meta information, e.g. `[ accession:'accession01' ]`
+  - name: file_name
+    type: file
+    description: "Input file to validate."
+
 output:
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing information on module software version
-          pattern: "versions.yml"
+  - name: versions
+    type: file
+    description: "File containing information on module software version."
+    pattern: "versions.yml"
+
 authors:
   - "ensembl-dev@ebi.ac.uk"
 maintainers:
diff --git a/modules/ensembl/metadata/amendgenome/meta.yml b/modules/ensembl/metadata/amendgenome/meta.yml
index 7864827..fe59eb0 100644
--- a/modules/ensembl/metadata/amendgenome/meta.yml
+++ b/modules/ensembl/metadata/amendgenome/meta.yml
@@ -1,57 +1,60 @@
 ---
 name: "metadata_amendgenome"
-description: Extends genome metadata using input files and validates the output against a genome schema.
+description: >
+  Extends genome metadata using input files and validates the output against
+  a genome schema.
 keywords:
   - amend
   - genome
-  - metada
+  - metadata
   - validation
 
 tools:
-  - "metadata_amendgenome":
-      description: "This module processes genome metadata by incorporating additional data from assembly reports and GenBank files, ensuring compliance with the genome schema"
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      licence: ['Apache License version 2.0']
+  metadata_amendgenome:
+    description: >
+      This module processes genome metadata by incorporating additional
+      data from assembly reports and GenBank files, ensuring compliance with the
+      genome schema
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
+    identifier: ""
 
 input:
-  - meta:
-      type: map
-      description: 
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession01' ]
-  - genome_json:
-      type: file
-      description: "JSON file containing genome metadata."
-      pattern: "*.json"
-  - asm_report:
-      type: file
-      description: "Assembly report file with genomic metadata."
-      pattern: "*.txt"
-  - genomic_fna:
-      type: file
-      description: "FASTA file containing genomic sequences."
-      pattern: "*.{fna,fasta,fa}"
-  
-  - genbank_gbff:
-      type: file
-      description: "GenBank file containing genome annotations."
-      pattern: "*.{gbff,gb}"
-  
+  - name: meta
+    type: map
+    description: >
+      Groovy Map containing meta information e.g. `[ accession:'accession01' ]`
+  - name: genome_json
+    type: file
+    description: "JSON file containing genome metadata."
+    pattern: "*.json"
+  - name: asm_report
+    type: file
+    description: "Assembly report file with genomic metadata."
+    pattern: "*.txt"
+  - name: genomic_fna
+    type: file
+    description: "FASTA file containing genomic sequences."
+    pattern: "*.{fna,fasta,fa}"
+  - name: genbank_gbff
+    type: file
+    description: "GenBank file containing genome annotations."
+    pattern: "*.{gbff,gb}"
+
 output:
-  - meta:
-      type: map
-      description: 
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession01' ]
-  - amended_json:
-      description: "JSON file containing genome metadata."
-      pattern: "*.json"
-  -  versions:
-      type: file
-      description: "File containing information on module software version."
-      pattern: "versions.yml"
-  
-  
+  - name: amended_json
+    type: map
+    description: >
+      Groovy Map containing meta information e.g. `[ accession:'accession01' ]`
+  - name: amended_json_file
+    type: file
+    description: "JSON file containing genome metadata."
+    pattern: "*.json"
+  - name: versions
+    type: file
+    description: "File containing information on module software version."
+    pattern: "versions.yml"
+
 authors:
   - "@ensembl-dev"
 maintainers:
diff --git a/modules/ensembl/metadata/genomesummary/meta.yml b/modules/ensembl/metadata/genomesummary/meta.yml
index f390100..c2b5b5f 100644
--- a/modules/ensembl/metadata/genomesummary/meta.yml
+++ b/modules/ensembl/metadata/genomesummary/meta.yml
@@ -1,7 +1,6 @@
 ---
 name: "metadata_genomesummary"
-description: Extract genome meta info from am NCBI datasets-cli 'genome summary' JSON.
-  A structured query JSON is also input and used to extract the key meta from the genome summary JSON.
+description: Extract genome meta info from an NCBI datasets-cli 'genome summary' JSON.
 keywords:
   - container
   - docker
@@ -9,48 +8,47 @@ keywords:
   - ensembl-genomio
   - genome
   - metadata
+
 tools:
-  - "metadata":
-      description: Modules which function to generate,fetch or otherwise work \
-        with metadata curation or preparation.
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
+  metadata:
+    description: Modules which function to generate, fetch or otherwise work \
+      with metadata curation or preparation.
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: ["Apache License version 2.0"]
 
 input:
-  - accession:
-      type: map
-      description: Meta map including sequence accession. Sequence record associated with 
-        NCBI accession (e.g. NC_0-9+, NM_0-9+, NT_0-9+, NP_0-9+)
-        e.g. [[ accession:'NC_12341']]
-  - input_query:
-      type: file
-      description: Input query to parse an NCBI genome summary JSON 
-      pattern: "*-query.json"
-  - genome_summary_json:
-      type: file
-      description: A genome summary JSON file downloaded via datasets-cli (NCBI) \
-        containing 1> genome summaries '{reports: {}}'
-      pattern: "*.json"
+  - name: accession
+    type: map
+    description: Meta map including sequence accession.
+
+  - name: input_query
+    type: file
+    description: Input query to parse an NCBI genome summary JSON
+    pattern: "*-query.json"
+
+  - name: genome_summary_json
+    type: file
+    description: |
+      A genome summary JSON file downloaded via datasets-cli (NCBI)
+    pattern: "*.json"
 
 output:
-  - meta:
-      type: map
-      description: |
-        Meta map including sequence accession. Sequence record associated with 
-        NCBI accession (e.g. NC_0-9+, NM_0-9+, NT_0-9+, NP_0-9+)
-        e.g. [[ accession:'NC_12341']]
-  - meta_json:
-    - "genome-meta.json":
-      type: file
-      description: Genome metadata queried from complete NCBI datasets genome summary JSON.
-      pattern: "*-meta.json"
-  - versions:
-    - "versions.yml":
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+  - name: meta
+    type: map
+    description: Meta map including sequence accession.
+
+  - name: meta_json
+    type: file
+    description: Genome metadata queried from JSON.
+    pattern: "*-meta.json"
+
+  - name: versions
+    type: file
+    description: File containing software versions
+    pattern: "versions.yml"
 
 authors:
   - "ensembl-dev@ebi.ac.uk"
+
 maintainers:
   - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/schema/json/meta.yml b/modules/ensembl/schema/json/meta.yml
new file mode 100644
index 0000000..e8d09ec
--- /dev/null
+++ b/modules/ensembl/schema/json/meta.yml
@@ -0,0 +1,48 @@
+---
+name: "schema_json"
+description: >
+  Validate the schema for JSON files.
+
+keywords:
+  - validate
+  - JSON
+  - schema
+
+tools:
+  Schema:
+    description: "Nextflow modules for Ensembl pipelines"
+    homepage: "https://github.com/Ensembl/nextflow_modules"
+    license: "Apache License 2.0"
+    identifier: ""
+
+input:
+  - name: meta
+    type: map
+    description: >
+      Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`
+
+  - name: json
+    type: file
+    description: JSON file to validate
+    pattern: "*.{json}"
+
+output:
+  - name: meta
+    type: map
+    description: >
+      Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`
+
+  - name: verified_json
+    type: file
+    description: Verified JSON file
+    pattern: "*.{json}"
+
+  - name: versions
+    type: file
+    description: File containing ensembl-genomio versions
+    pattern: "versions.yml"
+
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"

From 17f933e8dedc40afc261a1ffedcdacece3bb8a98 Mon Sep 17 00:00:00 2001
From: dishalodha <dishalodha@ebi.ac.uk>
Date: Tue, 17 Mar 2026 16:01:15 +0000
Subject: [PATCH 26/26] create a touch file

---
 modules/ensembl/annotation/dumpanno/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/ensembl/annotation/dumpanno/main.nf b/modules/ensembl/annotation/dumpanno/main.nf
index 0c26e02..e26a678 100644
--- a/modules/ensembl/annotation/dumpanno/main.nf
+++ b/modules/ensembl/annotation/dumpanno/main.nf
@@ -50,7 +50,7 @@ process ANNOTATION_DUMPANNO {
     stub:
         version = "0.4"
         """
-        echo "No change, create an empty json file" > functional_annotation.json
+        touch functional_annotation.json
 
         # Get version from genomio please
         echo -e -n "${task.process}:\n\tensembl-legacy-scripts:e112_APIv0.4 : $version" > versions.yml