diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml
index 8cfd0348..84bfc3db 100644
--- a/.github/workflows/linting.yaml
+++ b/.github/workflows/linting.yaml
@@ -1,5 +1,5 @@
 name: Run Linting
-on: [push, pull_request]
+on: {}
 
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
diff --git a/.github/workflows/nf-test.yaml b/.github/workflows/nf-test.yaml
index 14dfa3f0..6c0f70e9 100644
--- a/.github/workflows/nf-test.yaml
+++ b/.github/workflows/nf-test.yaml
@@ -1,5 +1,16 @@
 name: NF Tests
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "**/meta.yml"
+
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - "**/meta.yml"
 
 env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
diff --git a/modules/ensembl/annotation/dumpanno/main.nf b/modules/ensembl/annotation/dumpanno/main.nf
index 0c26e02c..14f9e1fd 100644
--- a/modules/ensembl/annotation/dumpanno/main.nf
+++ b/modules/ensembl/annotation/dumpanno/main.nf
@@ -24,7 +24,7 @@ process ANNOTATION_DUMPANNO {
 
     output:
         tuple val(db), val("functional_annotation"), path("*.json"), emit: functional_annotation
-        path "versions.yml", emit: versions
+        path "versions.yml", emit: versions, topic: versions
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/annotation/dumpanno/meta.yml b/modules/ensembl/annotation/dumpanno/meta.yml
index e474f326..c32f1666 100644
--- a/modules/ensembl/annotation/dumpanno/meta.yml
+++ b/modules/ensembl/annotation/dumpanno/meta.yml
@@ -1,51 +1,41 @@
----
-name: "annotation_dumpanno"
-
-description: This module is used to dump the functional annotation of a genome from core databases.
-
+name: annotation_dumpanno
+description: This module is used to dump the functional annotation of a genome from
+  core databases.
 keywords:
-  - container
-  - core_database
-  - docker
-  - ensembl-legacy-scripts
-  - fasta
-  
+- container
+- core_database
+- 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']
-
+- 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
+    licence:
+    - Apache License version 2.0
 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:
+    type: map
+    description: Channel element 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"
-
-  - versions:
+  functional_annotation:
+  - - db:
+        type: map
+        description: Channel element db.
+    - functional_annotation:
+        type: string
+        description: Channel element functional_annotation.
+    - '*.json':
+        type: file
+        description: Channel element *.json.
+        pattern: '*.json'
+  versions:
+  - versions.yml:
       type: file
       description: File containing software versions.
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
+- '@ensembl-dev'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'
diff --git a/modules/ensembl/annotation/dumpanno/tests/main.nf.test b/modules/ensembl/annotation/dumpanno/tests/main.nf.test
index 02d526ce..ff546079 100644
--- a/modules/ensembl/annotation/dumpanno/tests/main.nf.test
+++ b/modules/ensembl/annotation/dumpanno/tests/main.nf.test
@@ -21,6 +21,8 @@ nextflow_process {
 
     tag "annotation"
     tag "annotation/dumpanno"
+    tag "modules_ensembl"
+    tag "modules"
 
        
     test("Dump functional annotation ") {
diff --git a/modules/ensembl/database/dbfactory/meta.yml b/modules/ensembl/database/dbfactory/meta.yml
index d0cb82f5..7c8848b1 100644
--- a/modules/ensembl/database/dbfactory/meta.yml
+++ b/modules/ensembl/database/dbfactory/meta.yml
@@ -1,41 +1,43 @@
----
-name: "database_dbfactory"
-description: Generate a list of one or more databases plus some associated meta table information.
-
+name: database_dbfactory
+description: Generate a list of one or more databases plus some associated meta table
+  information.
 keywords:
-  - container
-  - core_database
-  - docker
-  - database
-  - ensembl-genomio
-
+- container
+- core_database
+- docker
+- database
+- 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
+    licence:
+    - Apache License version 2.0
 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:
+- - server:
       type: map
-      description: "Prefix to filter core databases. [default: none]"
+      description: 'Groovy Map containing MySQL server host, port, user and password
 
+        metadata, plus the JSON database filter information.
+
+        Example: [[ host:"mysql-host-test-prod" ], [ filter_map:"dbrename_re" ]]
+
+        '
+  - filter_map:
+      type: map
+      description: Channel element filter_map.
 output:
-  - dbs_meta_json:
+  dbs_meta_json:
+  - dbs.json:
       type: file
-      description: "JSON file containing database metadata."
-      pattern: "dbs.json"  
-  - versions:
+      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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/download/assemblydata/meta.yml b/modules/ensembl/download/assemblydata/meta.yml
index 0f93a868..82bfb905 100644
--- a/modules/ensembl/download/assemblydata/meta.yml
+++ b/modules/ensembl/download/assemblydata/meta.yml
@@ -1,46 +1,135 @@
----
-name: "download_assemblydata"
-description: Generate a list of one or more databases plus some associated meta table information.
-
+name: download_assemblydata
+description: Generate a list of one or more databases plus some associated meta table
+  information.
 keywords:
-  - ensembl-genomio
-  - container
-  - docker
-  - download
-  - genome
-  - gzip
-  - INSDC
-
+- ensembl-genomio
+- container
+- docker
+- download
+- genome
+- gzip
+- 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
+    licence:
+    - Apache License version 2.0
 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)
-  - versions:
+  min_set:
+  - - meta:
+        type: map
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_assembly_report.txt':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_genomic.fna.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+    - '*_genomic.gbff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .fna,
+
+          .gbff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.fna.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,fna.gz,gbff.gz}'
+  opt_set:
+  - - meta:
+        type: map
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_genomic.gff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_protein.faa.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+    - '*_genomic.gbff.gz':
+        type: file
+        description: 'Groovy Map including various genome assembly data files (.txt,
+          .faa,
+
+          .gff) into compressed Gzip archives.
+
+          Example: [ accession:''GCA_000000000.1'', file("*_assembly_report.txt"),
+          file("*_genomic.gff.gz"), file("*_genomic.gbff.gz") ]
+
+          '
+        pattern: '*.{txt,gff.gz,gbff.gz}'
+  versions:
+  - versions.yml:
       type: file
       description: File containing information on module software version
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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 79b8e316..cff9526d 100644
--- a/modules/ensembl/download/genbank/meta.yml
+++ b/modules/ensembl/download/genbank/meta.yml
@@ -1,39 +1,39 @@
----
-name: "download_genbank"
+name: download_genbank
 description: Download a single sequence from NCBI GenBank.
-
 keywords:
-  - core_database
-  - container
-  - docker
-  - ensembl-genomio
-  - genbank
-  - genomics
-
+- core_database
+- container
+- docker
+- ensembl-genomio
+- genbank
+- 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
+    licence:
+    - 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']]
-
+- meta:
+    type: map
+    description: Channel element meta.
 output:
-  - gb_sequence:
-      type: file
-      description: A sequence record outfile in genbank format.
-      pattern: "output.gb"
-  - versions:
+  gb_sequence:
+  - - meta:
+        type: map
+        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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/dump/genomestats/meta.yml b/modules/ensembl/dump/genomestats/meta.yml
index 65ebf0ac..77db4c74 100644
--- a/modules/ensembl/dump/genomestats/meta.yml
+++ b/modules/ensembl/dump/genomestats/meta.yml
@@ -1,38 +1,54 @@
----
-name: "dump_genomestats"
+name: dump_genomestats
 description: A module for dumping a core database
 keywords:
-  - container
-  - core_database
-  - docker
-  - ensembl-genomio
-  - json
-
+- container
+- core_database
+- docker
+- ensembl-genomio
+- 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
+    licence:
+    - Apache License version 2.0
 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 the core database name.
 
+      Example: [[ 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:
+  core_stats:
+  - - db:
+        type: map
+        description: 'JSON file containing core database statistics (assembly and
+          annotation).
+
+          Example: [ db:"database name", file("core_stats.json") ]
+
+          '
+        pattern: core_stats.json
+    - core_stats.json:
+        type: file
+        description: 'JSON file containing core database statistics (assembly and
+          annotation).
+
+          Example: [ 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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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 09f29c11..8275d067 100644
--- a/modules/ensembl/fasta/dumpfastanuc/meta.yml
+++ b/modules/ensembl/fasta/dumpfastanuc/meta.yml
@@ -1,40 +1,61 @@
----
-name: "fasta_dumpfastanuc"
+name: fasta_dumpfastanuc
 description: A module for dumping core database gene module nucleotide fasta seqs
-
 keywords:
-  - container
-  - database
-  - docker
-  - ensembl-genomio
-  - ensembl-legacy-scripts
-  - fasta
-
+- container
+- database
+- docker
+- ensembl-genomio
+- ensembl-legacy-scripts
+- 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/retrieval of
+      fasta sequences.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 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 the core database name.
 
+      Example: [[ 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:
+  nucleotide_fasta:
+  - - db:
+        type: map
+        description: 'FASTA file containing nucleotide sequence(s).
+
+          Example: [ db:''database name'', file("*_fasta_dna.fasta") ]
+
+          '
+        pattern: '*_fasta_dna.fasta'
+    - fasta_dna:
+        type: string
+        description: 'FASTA file containing nucleotide sequence(s).
+
+          Example: [ db:''database name'', file("*_fasta_dna.fasta") ]
+
+          '
+        pattern: '*_fasta_dna.fasta'
+    - '*.fasta':
+        type: file
+        description: 'FASTA file containing nucleotide sequence(s).
+
+          Example: [ 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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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 a4f81eb1..a29cf35d 100644
--- a/modules/ensembl/fasta/dumpfastapeptide/meta.yml
+++ b/modules/ensembl/fasta/dumpfastapeptide/meta.yml
@@ -1,40 +1,61 @@
----
-name: "fasta_dumpfastapeptide"
+name: fasta_dumpfastapeptide
 description: A module for dumping peptide FASTA sequences from core databases
-
 keywords:
-  - container
-  - database
-  - docker
-  - ensembl-genomio
-  - ensembl-legacy-scripts
-  - fasta
-
+- container
+- database
+- docker
+- ensembl-genomio
+- ensembl-legacy-scripts
+- 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/retrieval of
+      fasta sequences.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 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 the core database name.
 
+      Example: [[ 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:
+  peptide_fasta:
+  - - db:
+        type: map
+        description: 'FASTA file containing peptide sequence(s).
+
+          Example: [ db:''database name'', file("*_fasta_pep.fasta") ]
+
+          '
+        pattern: '*_fasta_pep.fasta'
+    - fasta_pep:
+        type: string
+        description: 'FASTA file containing peptide sequence(s).
+
+          Example: [ db:''database name'', file("*_fasta_pep.fasta") ]
+
+          '
+        pattern: '*_fasta_pep.fasta'
+    - '*.fasta':
+        type: file
+        description: 'FASTA file containing peptide sequence(s).
+
+          Example: [ 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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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/recombine/main.nf b/modules/ensembl/fasta/recombine/main.nf
index d0ae2406..1f1d1957 100644
--- a/modules/ensembl/fasta/recombine/main.nf
+++ b/modules/ensembl/fasta/recombine/main.nf
@@ -27,7 +27,7 @@ process FASTA_RECOMBINE {
         record(meta: Map, fasta_manifest: Path, agp: Path?)
 
     output:
-        record(meta: meta, recombined_fasta: file("${meta.id}.fa"))
+        recombined_fasta = record(meta: meta, recombined_fasta: file("${meta.id}.fa"))
 
     topic:
         tuple(task.process, 'fasta_recombine', eval("fasta_recombine --version 2>/dev/null || echo unknown")) >> 'versions'
diff --git a/modules/ensembl/fasta/recombine/tests/main.nf.test.snap b/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
index 59a7453a..00fbc19d 100644
--- a/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
+++ b/modules/ensembl/fasta/recombine/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                         },
                         "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
                     }
+                ],
+                "recombined_fasta": [
+                    {
+                        "meta": {
+                            "id": "test"
+                        },
+                        "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:53:47.242818",
+        "timestamp": "2026-10-19T12:18:14.056577866",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     },
     "stub outputs: header mode": {
@@ -28,13 +36,21 @@
                         },
                         "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
                     }
+                ],
+                "recombined_fasta": [
+                    {
+                        "meta": {
+                            "id": "test"
+                        },
+                        "recombined_fasta": "test.fa:md5,c40116e7d725da4662e6bdd654f70075"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:53:44.690151",
+        "timestamp": "2026-10-19T12:18:11.23778328",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/fasta/split/main.nf b/modules/ensembl/fasta/split/main.nf
index 1fb560cc..a9cd0edc 100644
--- a/modules/ensembl/fasta/split/main.nf
+++ b/modules/ensembl/fasta/split/main.nf
@@ -26,7 +26,7 @@ process FASTA_SPLIT {
         record(meta: Map, fasta: Path, longest_seq_bp: Long)
 
     output:
-        record(
+        split = record(
             meta: meta,
             fastas: files("splits/**/*.fa"),
             agp: file("splits/*.agp", optional: true)
@@ -35,7 +35,6 @@ process FASTA_SPLIT {
     topic:
         tuple(task.process, 'fasta_split', eval("fasta_split --version 2>/dev/null || echo unknown")) >> 'versions'
 
-
     script:
         def args = []
 
diff --git a/modules/ensembl/fasta/split/meta.yml b/modules/ensembl/fasta/split/meta.yml
index ec2c04b7..74f6ca96 100644
--- a/modules/ensembl/fasta/split/meta.yml
+++ b/modules/ensembl/fasta/split/meta.yml
@@ -31,25 +31,19 @@ input:
         description: Length in base pairs of the longest sequence in the input
           FASTA.
 output:
-  fastas:
+  split:
     - - meta:
           type: map
           description: |
             Groovy Map containing meta information
             e.g. `[ id:'accession1' ]`
-      - splits/**/*.fa:
+      - fastas:
           type: file
           description: Split FASTA files.
           pattern: "splits/**/*.fa"
           ontologies:
             - edam: "http://edamontology.org/format_1929" # FASTA
-  agp:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing meta information
-            e.g. `[ id:'accession1' ]`
-      - splits/*.agp:
+      - agp:
           type: file
           description: Optional AGP file describing split sequence chunks.
           pattern: "splits/*.agp"
diff --git a/modules/ensembl/fasta/stats/main.nf b/modules/ensembl/fasta/stats/main.nf
index 3456982d..b6287b3c 100644
--- a/modules/ensembl/fasta/stats/main.nf
+++ b/modules/ensembl/fasta/stats/main.nf
@@ -27,7 +27,7 @@ process FASTA_STATS {
         record(meta: Map, fasta: Path)
 
     output:
-        record(meta: meta, stats: file("${fasta.simpleName}.stats.json"))
+        stats = record(meta: meta, stats: file("${fasta.simpleName}.stats.json"))
 
     topic:
         tuple(task.process, 'fasta_stats', eval("fasta_stats --version 2>/dev/null || echo unknown")) >> 'versions'
diff --git a/modules/ensembl/fasta/stats/tests/main.nf.test.snap b/modules/ensembl/fasta/stats/tests/main.nf.test.snap
index e2bbf566..c2d57614 100644
--- a/modules/ensembl/fasta/stats/tests/main.nf.test.snap
+++ b/modules/ensembl/fasta/stats/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                         },
                         "stats": "input.stats.json:md5,d41d8cd98f00b204e9800998ecf8427e"
                     }
+                ],
+                "stats": [
+                    {
+                        "meta": {
+                            "id": "test"
+                        },
+                        "stats": "input.stats.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:53:55.741606",
+        "timestamp": "2026-10-19T12:20:59.659318033",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/features/combine_json/main.nf b/modules/ensembl/features/combine_json/main.nf
index bf4488d2..356fac26 100644
--- a/modules/ensembl/features/combine_json/main.nf
+++ b/modules/ensembl/features/combine_json/main.nf
@@ -31,7 +31,7 @@ process FEATURES_COMBINE_JSON {
         )
 
     output:
-        record(meta: meta, combined_json: file("${meta.id}.${analysis}.json"))
+        combined_json = record(meta: meta, combined_json: file("${meta.id}.${analysis}.json"))
 
     topic:
         tuple(task.process, 'features_combine_json', eval("features_combine_json --version 2>/dev/null || echo unknown")) >> 'versions'
diff --git a/modules/ensembl/features/combine_json/tests/main.nf.test.snap b/modules/ensembl/features/combine_json/tests/main.nf.test.snap
index 795b77f1..7d790925 100644
--- a/modules/ensembl/features/combine_json/tests/main.nf.test.snap
+++ b/modules/ensembl/features/combine_json/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "combined_json": [
+                    {
+                        "combined_json": "test.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:53:58.29327",
+        "timestamp": "2026-10-19T12:23:49.238647631",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/features/convert_to_json/main.nf b/modules/ensembl/features/convert_to_json/main.nf
index daa640ab..f1e32a49 100644
--- a/modules/ensembl/features/convert_to_json/main.nf
+++ b/modules/ensembl/features/convert_to_json/main.nf
@@ -33,7 +33,7 @@ process FEATURES_CONVERT_TO_JSON {
         )
 
     output:
-        record(meta: meta, features_json: file("${meta.id}.${analysis_logic_name}.features.json"))
+        features_json = record(meta: meta, features_json: file("${meta.id}.${analysis_logic_name}.features.json"))
 
     topic:
         tuple(task.process, 'features_convert_to_genomio_json', eval("features_convert_to_genomio_json --version 2>/dev/null || echo unknown")) >> 'versions'
diff --git a/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap b/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
index 0dc7c071..97aa3a9e 100644
--- a/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
+++ b/modules/ensembl/features/convert_to_json/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "features_json": [
+                    {
+                        "features_json": "test.repeatmask_customlib.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:54:04.437296",
+        "timestamp": "2026-10-19T12:23:58.024921293",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     },
     "Stub wires RepeatMasker Repbase input mode": {
@@ -28,13 +36,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "features_json": [
+                    {
+                        "features_json": "test.repeatmasker_repbase.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:54:02.363885",
+        "timestamp": "2026-10-19T12:23:55.069267917",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     },
     "Stub wires TRF input mode": {
@@ -47,13 +63,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "features_json": [
+                    {
+                        "features_json": "test.trf.features.json:md5,8a80554c91d9fca8acb82f023de02f11",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:54:00.329076",
+        "timestamp": "2026-10-19T12:23:52.218780934",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/features/red/main.nf b/modules/ensembl/features/red/main.nf
index 3ab40fb2..a746c1ea 100644
--- a/modules/ensembl/features/red/main.nf
+++ b/modules/ensembl/features/red/main.nf
@@ -26,7 +26,7 @@ process FEATURES_RED {
         record(meta: Map, fasta: Path)
 
     output:
-        record(meta: meta, bed: file("rpt/*.bed"))
+        bed = record(meta: meta, bed: file("rpt/*.bed"))
 
     topic:
         tuple(task.process, 'red', eval("conda list red --json | python -c 'import sys,json; print(json.load(sys.stdin)[0][\"version\"])' || echo 2.0")) >> 'versions'
diff --git a/modules/ensembl/features/red/tests/main.nf.test.snap b/modules/ensembl/features/red/tests/main.nf.test.snap
index 7648c3c3..06561c62 100644
--- a/modules/ensembl/features/red/tests/main.nf.test.snap
+++ b/modules/ensembl/features/red/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "bed": [
+                    {
+                        "bed": "test.bed:md5,aa604b48150afc506072a1f9656b6bb7",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:54:06.783701",
+        "timestamp": "2026-10-19T12:24:00.376023273",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 514b040a..fba2d48f 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -26,7 +26,7 @@ process FEATURES_TRF {
         record(meta: Map, fasta: Path)
 
     output:
-        record(meta: meta, dat: file("*.dat"))
+        dat = record(meta: meta, dat: file("*.dat"))
 
     topic:
         tuple(task.process, 'trf', eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0")) >> 'versions'
diff --git a/modules/ensembl/features/trf/tests/main.nf.test.snap b/modules/ensembl/features/trf/tests/main.nf.test.snap
index 92300cd3..1091add2 100644
--- a/modules/ensembl/features/trf/tests/main.nf.test.snap
+++ b/modules/ensembl/features/trf/tests/main.nf.test.snap
@@ -9,13 +9,21 @@
                             "id": "test"
                         }
                     }
+                ],
+                "dat": [
+                    {
+                        "dat": "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917",
+                        "meta": {
+                            "id": "test"
+                        }
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-29T12:54:08.817888",
+        "timestamp": "2026-10-19T12:24:02.655480303",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/genbank/extractgb/meta.yml b/modules/ensembl/genbank/extractgb/meta.yml
index 9ddcd0fc..e588d5c1 100644
--- a/modules/ensembl/genbank/extractgb/meta.yml
+++ b/modules/ensembl/genbank/extractgb/meta.yml
@@ -1,60 +1,87 @@
----
-name: "genbank_extractgb"
-description: Parse a GenBank file and create cleaned up files and validate generated JSON files. 
-
+name: genbank_extractgb
+description: Parse a GenBank file and create cleaned up files and validate generated
+  JSON files.
 keywords:
-  - container
-  - database
-  - docker
-  - ensembl-genomio
-  - genbank
-  - genomics
-
+- container
+- database
+- docker
+- ensembl-genomio
+- genbank
+- 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 work with Genbank related data
+      files.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - meta:
       type: map
-      description: |
-        Groovy Map containing genome database meta information
-        e.g. `[ accession:'NC_XXXX.X' ]`
+      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)
+      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:
+  genome:
+  - - meta:
+        type: map
+        description: Genome metadata (JSON)
+        pattern: genome.json
+    - genome.json:
+        type: file
+        description: Genome metadata (JSON)
+        pattern: genome.json
+  seq_regions:
+  - - meta:
+        type: map
+        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: map
+        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: map
+        description: Gene model information (GFF3)
+        pattern: '*.gff'
+    - '*.gff':
+        type: file
+        description: Gene model information (GFF3)
+        pattern: '*.gff'
+  pep_fasta:
+  - - meta:
+        type: map
+        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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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 1d27a3c3..2a228f71 100644
--- a/modules/ensembl/gff3/dumpgff3/meta.yml
+++ b/modules/ensembl/gff3/dumpgff3/meta.yml
@@ -1,39 +1,60 @@
----
-name: "gff3_dumpgff3"
+name: gff3_dumpgff3
 description: write your description here
-
 keywords:
-  - container
-  - database
-  - docker
-  - ensembl-legacy-scripts
-  - gff3
-
+- container
+- database
+- docker
+- ensembl-legacy-scripts
+- 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
+    licence:
+    - Apache License version 2.0
 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 the core database name.
 
+      Example: [[ 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:
+  gff3:
+  - - db:
+        type: map
+        description: 'GFF3 file containing gene model(s).
+
+          Example: [ db:''database name'', file("*.gff3") ]
+
+          '
+        pattern: '*.gff3'
+    - gff3:
+        type: string
+        description: 'GFF3 file containing gene model(s).
+
+          Example: [ db:''database name'', file("*.gff3") ]
+
+          '
+        pattern: '*.gff3'
+    - '*.gff3':
+        type: file
+        description: 'GFF3 file containing gene model(s).
+
+          Example: [ db:''database name'', file("*.gff3") ]
+
+          '
+        pattern: '*.gff3'
+  versions:
+  - versions.yml:
       type: file
       description: File containing information on module software version
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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 344861b4..f356540c 100644
--- a/modules/ensembl/gff3/validation/meta.yml
+++ b/modules/ensembl/gff3/validation/meta.yml
@@ -1,49 +1,50 @@
----
-name: "gff3_validation"
+name: gff3_validation
 description: Check for proper validation of the GFF3 using GenomeTools.
-
 keywords:
-  - ensembl
-  - integrity
-  - genomics
-  - genomio
-  - gff3
-  - validation
-
+- ensembl
+- integrity
+- genomics
+- genomio
+- gff3
+- 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
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - meta:
       type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
-  
+      description: 'Groovy Map containing meta information
+
+        e.g. `[ id:''accession1'' ]`
+
+        '
   - gene_models:
       type: file
       description: GFF3 files
-      pattern: "*.{gff3}"
-
+      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:
+  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"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/infernal/cmscan/main.nf b/modules/ensembl/infernal/cmscan/main.nf
index 9cea45fe..65dd7c4d 100644
--- a/modules/ensembl/infernal/cmscan/main.nf
+++ b/modules/ensembl/infernal/cmscan/main.nf
@@ -19,9 +19,7 @@ process CMSCAN {
     label 'process_high'
 
     conda "bioconda::infernal=1.1.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/infernal:1.1.5--pl5321h7b50bb2_4' :
-        'quay.io/biocontainers/infernal:1.1.5--pl5321h7b50bb2_4' }"
+    container "quay.io/biocontainers/infernal:1.1.5--pl5321h7b50bb2_4"
 
     input:
         record(
@@ -31,17 +29,13 @@ process CMSCAN {
         )
 
     output:
-        record(
+        tblout = record(
             meta:   meta,
             tblout: file("*.tblout")
         )
 
     topic:
-        tuple(
-            task.process,
-            'infernal',
-            eval("cmscan -h 2>&1 | sed -nE 's/^# INFERNAL ([^ ]+).*/\\1/p'")
-        ) >> 'versions'
+        tuple('cmscan', eval("cmscan --version 2>/dev/null || echo unknown")) >> 'versions'
 
     script:
         def prefix = task.ext.prefix
diff --git a/modules/ensembl/infernal/cmscan/meta.yml b/modules/ensembl/infernal/cmscan/meta.yml
index 50fb7ec3..7d59f469 100644
--- a/modules/ensembl/infernal/cmscan/meta.yml
+++ b/modules/ensembl/infernal/cmscan/meta.yml
@@ -12,6 +12,9 @@ tools:
       homepage: http://eddylab.org/infernal/
       documentation: http://eddylab.org/infernal/
       licence: ["BSD-3-Clause"]
+
+authors:
+  - "@ensembl-dev"
 input:
   - - meta:
         type: map
@@ -33,8 +36,12 @@ output:
           type: file
           description: Tabular cmscan hits for the input chunk.
           pattern: "*.tblout"
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions.
-        pattern: "versions.yml"
+    - - cmscan:
+          type: string
+          description: The name of the tool.
+      - ? cmscan --version 2>/dev/null || echo unknown
+        : type: eval
+          description: The expression to obtain the version of the tool.
diff --git a/modules/ensembl/infernal/cmscan/tests/main.nf.test b/modules/ensembl/infernal/cmscan/tests/main.nf.test
index e30908ab..336709cc 100644
--- a/modules/ensembl/infernal/cmscan/tests/main.nf.test
+++ b/modules/ensembl/infernal/cmscan/tests/main.nf.test
@@ -62,7 +62,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.size() == 1 },
+                { assert process.out.size() == 2 },
                 { assert process.out[0][0].meta.id == 'test' },
                 { assert path(process.out[0][0].tblout instanceof List ? process.out[0][0].tblout[0] : process.out[0][0].tblout).fileName.toString().endsWith('.tblout') },
                 { assert snapshot(process.out).match() }
diff --git a/modules/ensembl/infernal/cmscan/tests/main.nf.test.snap b/modules/ensembl/infernal/cmscan/tests/main.nf.test.snap
index be701214..913b631a 100644
--- a/modules/ensembl/infernal/cmscan/tests/main.nf.test.snap
+++ b/modules/ensembl/infernal/cmscan/tests/main.nf.test.snap
@@ -9,10 +9,18 @@
                         },
                         "tblout": "test.1.tblout:md5,d41d8cd98f00b204e9800998ecf8427e"
                     }
+                ],
+                "tblout": [
+                    {
+                        "meta": {
+                            "id": "test"
+                        },
+                        "tblout": "test.1.tblout:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    }
                 ]
             }
         ],
-        "timestamp": "2026-09-25T18:22:53.008883237",
+        "timestamp": "2026-10-19T12:25:58.306427968",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"
diff --git a/modules/ensembl/manifest/integrity/meta.yml b/modules/ensembl/manifest/integrity/meta.yml
index 44b8ec6a..6388ea27 100644
--- a/modules/ensembl/manifest/integrity/meta.yml
+++ b/modules/ensembl/manifest/integrity/meta.yml
@@ -1,57 +1,61 @@
----
-name: "manifest_integrity"
+name: manifest_integrity
 description: Check the data integrity of a set of genomic files, listed by their manifest.
 keywords:
-  - ensembl
-  - genomics
-  - genomio
-  - integrity
-  - validation
-
+- ensembl
+- genomics
+- genomio
+- integrity
+- 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
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - meta:
       type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
+      description: 'Groovy Map containing meta information
+
+        e.g. `[ id:''accession1'' ]`
+
+        '
   - manifest_files:
       type: file
       description: Set of genomic data files
-      pattern: "*.{gff3,fasta,json}"
-
+      pattern: '*.{gff3,fasta,json}'
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ id:'accession1' ]`
+  all_files:
+  - - meta:
+        type: map
+        description: 'Groovy Map containing meta information
 
-  - all_files:
-      type: file
-      description: All files used as entry.
-      pattern: "*.{gff3,fasta,json}"
+          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"
+          '
+    - '*.*':
+        type: file
+        description: All files used as entry.
+        pattern: '*.{gff3,fasta,json}'
+  error_log:
+  - - meta:
+        type: map
+        description: 'Groovy Map containing meta information
 
-  - error_log:
-      type: file
-      description: Integrity error log if it failed
-      pattern: "integrity.out"
-  - versions:
+          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"
-
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
+- '@ensembl-dev'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'
diff --git a/modules/ensembl/manifest/maker/main.nf b/modules/ensembl/manifest/maker/main.nf
index 41ef1136..958816d8 100644
--- a/modules/ensembl/manifest/maker/main.nf
+++ b/modules/ensembl/manifest/maker/main.nf
@@ -25,7 +25,7 @@ process MANIFEST_MAKER {
         tuple val(meta), path(file_name)
 
     output:
-        tuple val(meta), path("*.{gff3,fasta,json}", includeInputs: true)
+        tuple val(meta), path("*.{gff3,fasta,json}", includeInputs: true), emit: manifest
         path "versions.yml", emit: versions
     
     when:
diff --git a/modules/ensembl/manifest/maker/meta.yml b/modules/ensembl/manifest/maker/meta.yml
index 0f56d39c..0b250ea2 100644
--- a/modules/ensembl/manifest/maker/meta.yml
+++ b/modules/ensembl/manifest/maker/meta.yml
@@ -1,50 +1,44 @@
----
-name: "manifest_maker"
-description: Generate a manifest and validate its JSON schema using provided input files and metadata.
+name: manifest_maker
+description: Generate a manifest and validate its JSON schema using provided input
+  files and metadata.
 keywords:
-  - ensembl
-  - genomics
-  - genomio
-  - integrity
-  - validation
+- 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
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - 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}"
+      description: 'Groovy Map containing meta information
 
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession1' ]`
+        e.g. `[ accession:''accession01'' ]`
 
-  - all_files:
-      type: file
-      description: All files used as entry
-      pattern: "*.{gff3,fasta,json}"
-  - error_log:
+        '
+  - file_name:
       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"
-
+      description: Channel element file_name.
+output:
+  manifest:
+    - - meta:
+          type: map
+          description: Groovy Map containing manifest metadata.
+      - '*.{gff3,fasta,json}':
+          type: file
+          description: Generated manifest and input files.
+          pattern: '*.{gff3,fasta,json}'
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing information on module software version.
+        pattern: 'versions.yml'
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- 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/manifest/maker/tests/main.nf.test.snap b/modules/ensembl/manifest/maker/tests/main.nf.test.snap
index fd7670c5..797c9253 100644
--- a/modules/ensembl/manifest/maker/tests/main.nf.test.snap
+++ b/modules/ensembl/manifest/maker/tests/main.nf.test.snap
@@ -14,15 +14,24 @@
                 "1": [
                     "versions.yml:md5,b2d9940151b29e7881ddbf8e3df6db49"
                 ],
+                "manifest": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "manifest.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,b2d9940151b29e7881ddbf8e3df6db49"
                 ]
             }
         ],
-        "timestamp": "2026-02-24T21:05:18.307649581",
+        "timestamp": "2026-10-19T12:28:43.967112538",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
         }
     },
     "Maker check stub": {
@@ -42,15 +51,26 @@
                 "1": [
                     "versions.yml:md5,b2d9940151b29e7881ddbf8e3df6db49"
                 ],
+                "manifest": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genes.gff3:md5,5e2fd50352e7d2ebec2bdccaa352e541",
+                            "manifest.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,b2d9940151b29e7881ddbf8e3df6db49"
                 ]
             }
         ],
-        "timestamp": "2026-02-24T21:05:04.068850359",
+        "timestamp": "2026-10-19T12:28:40.977854791",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
         }
     }
 }
\ No newline at end of file
diff --git a/modules/ensembl/metadata/amendgenome/meta.yml b/modules/ensembl/metadata/amendgenome/meta.yml
index 7864827f..9bb45503 100644
--- a/modules/ensembl/metadata/amendgenome/meta.yml
+++ b/modules/ensembl/metadata/amendgenome/meta.yml
@@ -1,58 +1,56 @@
----
-name: "metadata_amendgenome"
-description: Extends genome metadata using input files and validates the output against a genome schema.
+name: metadata_amendgenome
+description: Extends genome metadata using input files and validates the output against
+  a genome schema.
 keywords:
-  - amend
-  - genome
-  - metada
-  - validation
-
+- amend
+- genome
+- metada
+- 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
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - meta:
       type: map
-      description: 
-        Groovy Map containing meta information
-        e.g. `[ accession:'accession01' ]
+      description: Groovy Map containing meta information e.g. `[ accession:'accession01'
+        ]
   - genome_json:
       type: file
-      description: "JSON file containing genome metadata."
-      pattern: "*.json"
+      description: JSON file containing genome metadata.
+      pattern: '*.json'
   - asm_report:
       type: file
-      description: "Assembly report file with genomic metadata."
-      pattern: "*.txt"
+      description: Assembly report file with genomic metadata.
+      pattern: '*.txt'
   - genomic_fna:
       type: file
-      description: "FASTA file containing genomic sequences."
-      pattern: "*.{fna,fasta,fa}"
-  
+      description: FASTA file containing genomic sequences.
+      pattern: '*.{fna,fasta,fa}'
   - genbank_gbff:
       type: file
-      description: "GenBank file containing genome annotations."
-      pattern: "*.{gbff,gb}"
-  
+      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:
+  amended_json:
+  - - meta:
+        type: map
+        description: Groovy Map containing meta information e.g. `[ accession:'accession01'
+          ]
+    - genome.json:
+        description: JSON file containing genome metadata.
+        pattern: '*.json'
+        type: file
+  versions:
+  - versions.yml:
       type: file
-      description: "File containing information on module software version."
-      pattern: "versions.yml"
-  
-  
+      description: File containing information on module software version.
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
+- '@ensembl-dev'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'
diff --git a/modules/ensembl/metadata/genomesummary/meta.yml b/modules/ensembl/metadata/genomesummary/meta.yml
index f3901006..107476bb 100644
--- a/modules/ensembl/metadata/genomesummary/meta.yml
+++ b/modules/ensembl/metadata/genomesummary/meta.yml
@@ -1,56 +1,57 @@
----
-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.
+name: metadata_genomesummary
+description: 'Extract genome metadata from an NCBI datasets-cli ''genome summary''
+  JSON.
+
+  A structured query JSON is also input and used to extract key metadata.
+
+  '
 keywords:
-  - container
-  - docker
-  - datasets
-  - ensembl-genomio
-  - genome
-  - metadata
+- container
+- docker
+- datasets
+- 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 generate, fetch, or otherwise work with metadata curation
+      or preparation.
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 input:
-  - accession:
+- - 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']]
+      description: Channel element meta.
   - input_query:
       type: file
-      description: Input query to parse an NCBI genome summary JSON 
-      pattern: "*-query.json"
+      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"
+      description: 'A genome summary JSON file downloaded via datasets-cli (NCBI),
+
+        containing one or more genome summaries.
 
+        '
+      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":
+  meta_json:
+  - - meta:
+        type: map
+        description: "Meta map including sequence accession. Sequence record associated\
+          \ with \nNCBI accession (e.g. NC_0-9+, NM_0-9+, NT_0-9+, NP_0-9+)\ne.g.\
+          \ [[ accession:'NC_12341']]\n"
+    - genome.json:
         type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-
+        description: Channel element genome.json.
+        pattern: genome.json
+  versions:
+  - versions.yml:
+      type: file
+      description: Channel element versions.yml.
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/schema/json/meta.yaml b/modules/ensembl/schema/json/meta.yaml
deleted file mode 100644
index c70ecc3e..00000000
--- a/modules/ensembl/schema/json/meta.yaml
+++ /dev/null
@@ -1,62 +0,0 @@
-# See the NOTICE file distributed with this work for additional information
-# regarding copyright ownership.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#      http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-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"
-      # documentation: ""
-      # tool_dev_url: ""
-      # doi: ""
-      licence: "Apache License 2.0"
-input:
-  # Only when we have meta
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  
-  - json:
-      type: file
-      description: JSON file to validate
-      pattern: "*.{json}"
-
-output:
-  # Only when we have meta
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  - versions:
-      type: file
-      description: File containing ensembl-genomio versions
-      pattern: "versions.yml"
-  - json:
-      type: file
-      description: verified_json file
-      pattern: "*.{json}"
-
-authors:
-  - "ensembl-dev@ebi.ac.uk"
-maintainers:
-  - "ensembl-dev@ebi.ac.uk"
\ No newline at end of file
diff --git a/modules/ensembl/schema/json/meta.yml b/modules/ensembl/schema/json/meta.yml
new file mode 100644
index 00000000..042f10f6
--- /dev/null
+++ b/modules/ensembl/schema/json/meta.yml
@@ -0,0 +1,44 @@
+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
+    licence:
+    - Apache License 2.0
+input:
+- - meta:
+      type: map
+      description: 'Groovy Map containing sample information
+
+        e.g. `[ id:''sample1'', single_end:false ]`
+
+        '
+  - json_file:
+      type: file
+      description: Channel element json_file.
+output:
+  verified_json:
+  - - meta:
+        type: map
+        description: 'Groovy Map containing sample information
+
+          e.g. `[ id:''sample1'', single_end:false ]`
+
+          '
+    - json_file:
+        type: file
+        description: Channel element json_file.
+  versions:
+  - versions.yml:
+      type: file
+      description: File containing ensembl-genomio versions
+      pattern: versions.yml
+authors:
+- ensembl-dev@ebi.ac.uk
+maintainers:
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/seqregion/processseqregions/meta.yml b/modules/ensembl/seqregion/processseqregions/meta.yml
index a135d0e2..a09297d7 100644
--- a/modules/ensembl/seqregion/processseqregions/meta.yml
+++ b/modules/ensembl/seqregion/processseqregions/meta.yml
@@ -1,55 +1,58 @@
----
-name: "seqregion_processseqregions"
+name: seqregion_processseqregions
 description: Construct a sequence region metadata file from INSDC files.
 keywords:
-  - container
-  - ensembl-genomio
-  - genomics
-  - sequence_regions
-  - validation
-
+- container
+- ensembl-genomio
+- genomics
+- sequence_regions
+- validation
 tools:
-  - "seqregion":
-      description: "Nextflow modules for sequence region validation"
-      homepage: "https://github.com/Ensembl/nextflow_modules"
-      license: ['Apache License version 2.0']
-
+- seqregion:
+    description: Nextflow modules for sequence region validation
+    homepage: https://github.com/Ensembl/nextflow_modules
+    licence:
+    - Apache License version 2.0
 input:
-  - meta:
+- - meta:
       type: map
-      description: |
-        Groovy Map containing meta information
-        e.g. `[ db: 'dummy_core_110_1', species:'homo_sapiens' ]`
+      description: 'Groovy Map containing meta information
+
+        e.g. `[ db: ''dummy_core_110_1'', species:''homo_sapiens'' ]`
+
+        '
   - genome_json:
       type: file
       description: JSON file containing assembly, annotation and taxonomy meta info
-      pattern: "genome.json"
+      pattern: genome.json
   - assembly_report:
       type: file
       description: Genome assembly report file assoicated with INSDC deposited assembly
-      pattern: "*_assembly_report.txt"
+      pattern: '*_assembly_report.txt'
   - genomic_gbff:
       type: file
-      description: Assoicated GBFF file with DDBJ/ENA/GenBank feature table linked 
+      description: Assoicated GBFF file with DDBJ/ENA/GenBank feature table linked
         to INSDC deposited assembly
-      pattern: "*.gbff.gz|*.gbff"
-
+      pattern: '*.gbff.gz|*.gbff'
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ db: 'dummy_core_110_1', species:'homo_sapiens' ]`
-  - seq_region:
-      type: file
-      description: Sole output file of sequence region metadata, validated with JSON 'seq_region' schema
-      pattern: "seq_region.json"
-  - versions:
+  seq_region:
+  - - meta:
+        type: map
+        description: 'Groovy Map containing sample information
+
+          e.g. `[ db: ''dummy_core_110_1'', species:''homo_sapiens'' ]`
+
+          '
+    - seq_region.json:
+        type: file
+        description: Sole output file of sequence region metadata, validated with
+          JSON 'seq_region' schema
+        pattern: seq_region.json
+  versions:
+  - versions.yml:
       type: file
       description: File containing software versions
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
 maintainers:
-  - "ensembl-dev@ebi.ac.uk"
+- ensembl-dev@ebi.ac.uk
diff --git a/modules/ensembl/urls/extract/meta.yml b/modules/ensembl/urls/extract/meta.yml
index beb0f0cb..142a09f7 100644
--- a/modules/ensembl/urls/extract/meta.yml
+++ b/modules/ensembl/urls/extract/meta.yml
@@ -1,49 +1,55 @@
----
-name: "URLS_EXTRACT"
+name: URLS_EXTRACT
 description: Extracts MySQL arguments from a URL string
 keywords:
-  - url
-  - mysql
-  - parse
-
+- url
+- mysql
+- parse
+tools:
+- urls:
+    description: Extract connection parameters from a MySQL URL.
+    homepage: https://github.com/Ensembl/nextflow_modules
 input:
-  - meta:
+- - meta:
       type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+      description: 'Groovy Map containing sample information
+
+        e.g. [ id:''test'', single_end:false ]
+
+        '
   - url_string:
       type: string
       description: MySQL URL string to parse
-
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - user:
-      type: string
-      description: Extracted username from the URL
-  - password:
-      type: string
-      description: Extracted password from the URL (if present)
-  - host:
-      type: string
-      description: Extracted host from the URL
-  - port:
-      type: string
-      description: Extracted port from the URL
-  - database:
-      type: string
-      description: Extracted database name from the URL (if present)
-  - versions:
+  connection_info:
+  - - meta:
+        type: map
+        description: 'Groovy Map containing sample information
+
+          e.g. [ id:''test'', single_end:false ]
+
+          '
+    - user:
+        type: string
+        description: Extracted username from the URL
+    - host:
+        type: string
+        description: Extracted host from the URL
+    - port:
+        type: string
+        description: Extracted port from the URL
+    - password:
+        type: string
+        description: Extracted password from the URL (if present)
+    - database:
+        type: string
+        description: Extracted database name from the URL (if present)
+  versions:
+  - versions.yml:
       type: file
       description: File containing software versions
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
-  - "@Salome-Brunon"
+- '@ensembl-dev'
+- '@Salome-Brunon'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'
diff --git a/modules/ensembl/urls/generate/meta.yml b/modules/ensembl/urls/generate/meta.yml
index b9d97ad0..dabffe43 100644
--- a/modules/ensembl/urls/generate/meta.yml
+++ b/modules/ensembl/urls/generate/meta.yml
@@ -1,18 +1,16 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "urls_generate"
+name: urls_generate
 description: Generates a URL for database connections based on input parameters
 keywords:
-  - url
-  - database
-  - connection
+- url
+- database
+- connection
 tools:
-  - bash:
-      description: The module uses Bash scripting to generate the URL
-      homepage: https://www.gnu.org/software/bash/
-      documentation: https://www.gnu.org/software/bash/manual/
+- bash:
+    description: The module uses Bash scripting to generate the URL
+    homepage: https://www.gnu.org/software/bash/
+    documentation: https://www.gnu.org/software/bash/manual/
 input:
-  - meta:
+- - meta:
       type: map
       description: Metadata map
   - protocol:
@@ -34,19 +32,20 @@ input:
       type: string
       description: The name of the database to connect to (optional)
 output:
-  - meta:
-      type: map
-      description: Metadata map
-  - base_url:
-      type: string
-      description: The generated URL for the database connection
-  - versions:
+  url_sql:
+  - - meta:
+        type: map
+        description: Metadata map
+    - base_url:
+        type: string
+        description: The generated URL for the database connection
+  versions:
+  - versions.yml:
       type: file
       description: File containing software versions
-      pattern: "versions.yml"
-
+      pattern: versions.yml
 authors:
-  - "@ensembl-dev"
-  - "@Salome-Brunon"
+- '@ensembl-dev'
+- '@Salome-Brunon'
 maintainers:
-  - "@ensembl-dev"
+- '@ensembl-dev'