diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
new file mode 100644
index 0000000..64576e1
--- /dev/null
+++ b/.github/workflows/linting.yaml
@@ -0,0 +1,105 @@
+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 }}
+  NXF_VER: "25.10.2"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  nf-core-changes:
+    name: Detect changes
+    runs-on: ubuntu-latest
+
+    outputs:
+      # 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: ${{ steps.subworkflow_names.outputs.result }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          
+      - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
+        id: filter
+        with:
+          filters: |
+            modules:
+              - added|modified: 'modules/ensembl/**'
+            subworkflows:
+              - added|modified: 'subworkflows/ensembl/**'
+          token: ""
+          list-files: "json"
+
+      - name: Get module name
+        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
+        id: module_names
+        with:
+          script: |
+            return [...new Set(${{ 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/nf-core/', '')
+                .replace(/\/(main\.nf|tests\/.*)$/, '')
+              )
+            )];
+
+      - name: debug
+        run: |
+          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
+    runs-on: ubuntu-latest
+    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:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.14"
+
+      - uses: actions/cache@v5
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-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: Lint modules
+        run: nf-core modules lint ${{ matrix.module }}
+
+      - name: Lint subworkflows
+        if: needs.nf-core-changes.outputs.subworkflows == 'true'
+        run: nf-core subworkflows lint --all
\ No newline at end of file
diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
new file mode 100644
index 0000000..d7b570c
--- /dev/null
+++ b/.github/workflows/nf-test.yaml
@@ -0,0 +1,48 @@
+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
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v4
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+
+      - name: Setup Nextflow latest
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "latest-stable"
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        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 
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
diff --git a/modules/ensembl/annotation/dumpanno/meta.yml b/modules/ensembl/annotation/dumpanno/meta.yml
index e474f32..4656902 100644
--- a/modules/ensembl/annotation/dumpanno/meta.yml
+++ b/modules/ensembl/annotation/dumpanno/meta.yml
@@ -1,51 +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']
+  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
-  - 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_*"
+  - name: server
+    type: map
+    description: >
+      Groovy Map containing MySQL server host, port, user, and password meta information,
+      e.g. `[ host:"mysql-host-test-prod" ]`
 
-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_*"
+  - name: filter_map
+    type: file
+    description: "JSON file containing database filter information."
+    pattern: "*.json"
 
-  - functional_annotation.json:
-      type: map
-      description: |
-        Functional annotation file containing biotypes.
-        e.g [ db:'database name', file("*.json") ]
-      pattern: ".json"
+output:
+  - name: dbs_meta
+    type: file
+    description: "JSON file containing database metadata."
+    pattern: "dbs.json"
 
-  - versions:
-      type: file
-      description: File containing software versions.
-      pattern: "versions.yml"
+  - 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 d0cb82f..4656902 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
@@ -10,30 +11,35 @@ 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']
+  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" ]]
-  - filtermap:
-      type: map
-      description: "Prefix to filter core databases. [default: none]"
+  - 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:
-      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"
+  - 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"
diff --git a/modules/ensembl/download/assemblydata/meta.yml b/modules/ensembl/download/assemblydata/meta.yml
index 0f93a86..16e2c39 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
@@ -12,35 +13,38 @@ 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']
+  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:
-      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)
-  - versions:
-      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:
-  - "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..153b23a 100644
--- a/modules/ensembl/download/genbank/meta.yml
+++ b/modules/ensembl/download/genbank/meta.yml
@@ -1,6 +1,7 @@
 ---
 name: "download_genbank"
-description: Download a single sequence from NCBI GenBank.
+description: >
+  Download a single sequence from NCBI GenBank.
 
 keywords:
   - core_database
@@ -11,27 +12,33 @@ 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']
+  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:
-  - 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']]
+  - name: meta
+    type: map
+    description: "Optional meta information about the sequence to download."
 
 output:
-  - gb_sequence:
-      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"
+  - 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"
diff --git a/modules/ensembl/dump/genomestats/meta.yml b/modules/ensembl/dump/genomestats/meta.yml
index 65ebf0a..80d5967 100644
--- a/modules/ensembl/dump/genomestats/meta.yml
+++ b/modules/ensembl/dump/genomestats/meta.yml
@@ -1,6 +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
@@ -9,30 +11,38 @@ 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']
+  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:
-      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"
+  - 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:
-  - "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..3ceff2b 100644
--- a/modules/ensembl/fasta/dumpfastanuc/meta.yml
+++ b/modules/ensembl/fasta/dumpfastanuc/meta.yml
@@ -1,6 +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
@@ -11,30 +12,39 @@ 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']
+  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:
-      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"
+  - 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:
-  - "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..c6feafd 100644
--- a/modules/ensembl/fasta/dumpfastapeptide/meta.yml
+++ b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
@@ -1,6 +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
@@ -11,30 +12,39 @@ 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']
+  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:
-      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"
+  - 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:
-  - "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..fd4d090 100644
--- a/modules/ensembl/genbank/extractgb/meta.yml
+++ b/modules/ensembl/genbank/extractgb/meta.yml
@@ -1,6 +1,8 @@
 ---
 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, validating generated
+  JSON files.
 
 keywords:
   - container
@@ -11,50 +13,54 @@ 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']
+  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:
-      type: file
-      description: Genome metadata (JSON)
-      pattern: "genome.json"
-  - seq_regions:
-      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"
-  - gene_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"
-  - versions:
-      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:
-  - "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..2aa4365 100644
--- a/modules/ensembl/gff3/dumpgff3/meta.yml
+++ b/modules/ensembl/gff3/dumpgff3/meta.yml
@@ -1,6 +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
@@ -10,30 +12,40 @@ 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']
+  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:
-      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"
+  - 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:
-  - "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..e7d8784 100644
--- a/modules/ensembl/gff3/validation/meta.yml
+++ b/modules/ensembl/gff3/validation/meta.yml
@@ -1,6 +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
@@ -11,37 +12,38 @@ 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']
+  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:
-  - 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}"
-  - versions:
-      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"
diff --git a/modules/ensembl/manifest/integrity/meta.yml b/modules/ensembl/manifest/integrity/meta.yml
index 44b8ec6..d18bfcf 100644
--- a/modules/ensembl/manifest/integrity/meta.yml
+++ b/modules/ensembl/manifest/integrity/meta.yml
@@ -1,6 +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
@@ -9,47 +10,46 @@ 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']
+  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:
-  - 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"
-
-  - 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"
+  - 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"
diff --git a/modules/ensembl/manifest/maker/meta.yml b/modules/ensembl/manifest/maker/meta.yml
index 0f56d39..1c3dece 100644
--- a/modules/ensembl/manifest/maker/meta.yml
+++ b/modules/ensembl/manifest/maker/meta.yml
@@ -1,50 +1,38 @@
 ---
 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
   - 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']
-      
+  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' ]`
-  - 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. `[ accession:'accession01' ]`
+  - name: file_name
+    type: file
+    description: "Input file to validate."
 
 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"
+  - name: versions
+    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/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"