diff --git a/.editorconfig b/.editorconfig
index 2951ad83077..d04d3b51538 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -13,3 +13,7 @@ indent_size = 2
 
 [*.nf.test]
 insert_final_newline = false
+
+# ignore Readme
+[README.md]
+indent_style = unset
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 5d7ff4887e2..32e5a35fab8 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -1,5 +1,4 @@
-name: fix-linting
-run-name: fix linting (automated)
+name: Fix linting from a comment
 on:
   issue_comment:
     types: [created]
@@ -14,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,40 +31,56 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
+        with:
+          node-version: 20
+      - run: npm install --only=dev
+
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
-          else
-            echo "::set-output name=result::fail"
-          fi
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Post nothing-to-do comment
-        if: steps.prettier_status.outputs.result == 'pass'
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: ${{ steps.pre-commit.outcome }} == 'success'
         uses: peter-evans/create-or-update-comment@v3
         with:
-          issue-number: ${{ github.event.issue.number }}
-          body: |
-            Nothing for me to do here! :shrug:
-            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+          comment-id: ${{ github.event.comment.id }}
+          reactions: green_check_mark
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: ${{ steps.pre-commit.outcome }} == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'success'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: pencil2
+
+      - name: react if linting errors were not fixed
+        if: ${{ steps.commit-and-push.outcome }} == 'failure'
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: x
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 354174ea269..8e0f94fc7ba 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -23,46 +23,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-      - uses: actions/setup-python@v3
-      - uses: pre-commit/action@v3.0.0
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c #v5
+      - name: Fetch master
+        run: |
+          git fetch --no-tags --prune --depth=1 origin +refs/heads/*:refs/remotes/origin/*
+
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507 # v3.0.0
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
         # easier to fix these as they come up rather than everything at once.
         with:
-          extra_args: ""
-
-  prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier@3.1.0
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  editorconfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
-
+          extra_args: " --files $(git diff --name-only master...)"
   pytest-changes:
     name: pytest-changes
     runs-on: ubuntu-latest
@@ -96,9 +67,6 @@ jobs:
         id: get_tags
         run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
 
-      - name: debug
-        run: cat .github/tags.yml
-
       # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
       - uses: mirpedrol/paths-filter@main
         id: filter
@@ -107,7 +75,7 @@ jobs:
           token: ""
 
   nf-core-lint:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: nf-core-lint
     needs: [pytest-changes, nf-test-changes]
     if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }}
@@ -126,13 +94,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
+          cache: "pip"
 
       - name: Install pip
         run: python -m pip install --upgrade pip
@@ -142,7 +104,7 @@ jobs:
           distribution: "temurin"
           java-version: "17"
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
 
       - name: Install nf-core tools development version
         run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
@@ -160,7 +122,7 @@ jobs:
         if: ${{ startsWith(matrix.tags, 'subworkflows/') }}
 
   pytest:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: pytest
     needs: [pytest-changes]
     if: needs.pytest-changes.outputs.modules != '[]'
@@ -374,6 +336,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
+          cache: "pip"
 
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow cryptography
@@ -383,7 +346,7 @@ jobs:
           distribution: "temurin"
           java-version: "17"
       - name: Setup Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
         with:
           version: "${{ matrix.NXF_VER }}"
 
@@ -401,6 +364,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: "latest"
+          auto-update-conda: true
           channels: conda-forge,bioconda,defaults
           python-version: ${{ matrix.python-version }}
 
@@ -459,7 +423,7 @@ jobs:
             !${{ github.workspace }}/.singularity
 
   nf-test:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     name: nf-test
     needs: [nf-test-changes]
     if: needs.nf-test-changes.outputs.modules != '[]'
@@ -578,20 +542,31 @@ jobs:
         with:
           distribution: "temurin"
           java-version: "17"
+
       - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: MillironX/setup-nextflow@feature/api-switch
+
+      - name: Look if nf-test is already installed and write to env variable
+        id: check-nftest
+        run: |
+          if [ -f /usr/local/bin/nf-test ]; then
+            echo "nftest_installed=true" >> $GITHUB_ENV
+          else
+            echo "nftest_installed=false" >> $GITHUB_ENV
+          fi
 
       - name: Cache nf-test installation
+        if: env.nftest_installed != 'true'
         id: cache-software
         uses: actions/cache@v3
         with:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-nftest-${{ env.date }}
 
       - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
+        if: steps.cache-software.outputs.cache-hit != 'true' && env.nftest_installed != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash
           sudo mv nf-test /usr/local/bin/
@@ -606,6 +581,11 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
       - name: Set up miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -619,9 +599,9 @@ jobs:
           conda clean -a
           conda install -n base conda-libmamba-solver
           conda config --set solver libmamba
-          pip install pdiff
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
+          python -m pip install --upgrade pip pdiff
 
       # Set up secrets
       - name: Set up nextflow secrets
@@ -655,7 +635,7 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    needs: [pre-commit, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
     if: always()
     steps:
       - name: All tests ok
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 88eb01c4034..427b96ed085 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,18 +3,35 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+        exclude: ".*(test).*"
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.27.0
     hooks:
       - id: check-jsonschema
+        name: check meta.yml's of modules
         # match meta.ymls in one of the subdirectories of modules/nf-core
         files: ^modules/nf-core/.*/meta\.yml$
-        args: ["--schemafile", "modules/yaml-schema.json"]
+        args: ["--schemafile", "modules/meta-schema.json"]
+      - id: check-jsonschema
+        name: check environment.yml's of modules
+        # match environment.ymls in one of the subdirectories of modules/nf-core
+        files: ^modules/nf-core/.*/environment\.yml$
+        args: ["--schemafile", "modules/environment-schema.json"]
       - id: check-jsonschema
+        name: check meta.yml's of subworkflows
         # match meta.ymls in one of the subdirectories of subworkflows/nf-core
         files: ^subworkflows/nf-core/.*/meta\.yml$
-        args: ["--schemafile", "subworkflows/yaml-schema.json"]
-      - id: check-github-workflows
+        args: ["--schemafile", "subworkflows/meta-schema.json"]
+      - id: check-jsonschema
+        name: check environment.yml's of subworkflows
+        # match environment.ymls in one of the subdirectories of subworkflows/nf-core
+        files: ^subworkflows/nf-core/.*/environment\.yml$
+        args: ["--schemafile", "subworkflows/environment-schema.json"]
   - repo: https://github.com/renovatebot/pre-commit-hooks
     rev: 37.127.0
     hooks:
diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml
index 47795117a66..c428f3d861d 100644
--- a/modules/nf-core/ampcombi/meta.yml
+++ b/modules/nf-core/ampcombi/meta.yml
@@ -18,7 +18,7 @@ tools:
       homepage: "https://github.com/Darcy220606/AMPcombi"
       documentation: "https://github.com/Darcy220606/AMPcombi"
       tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -26,10 +26,10 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - amp_input:
-      type: folder or filelist
+      type: directory
       description: The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.
   - faa_input:
-      type: folder or file
+      type: directory
       description: The path to the folder or file corresponding to the respective protein fasta files with '.faa' extension. Filenames have to contain the corresponding sample-name, i.e. sample_1.faa
       pattern: "*/"
   - amp_database:
diff --git a/modules/nf-core/angsd/docounts/meta.yml b/modules/nf-core/angsd/docounts/meta.yml
index 8381091f9c6..6a41ff53f32 100644
--- a/modules/nf-core/angsd/docounts/meta.yml
+++ b/modules/nf-core/angsd/docounts/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "http://www.popgen.dk/angsd/"
       tool_dev_url: "https://github.com/ANGSD/angsd"
       doi: "10.1186/s12859-014-0356-4"
-      licence: "['GPL v3, MIT']"
+      licence: ["GPL v3", "MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/annotsv/annotsv/meta.yml b/modules/nf-core/annotsv/annotsv/meta.yml
index 20685d5f2c9..b98a5132fcd 100644
--- a/modules/nf-core/annotsv/annotsv/meta.yml
+++ b/modules/nf-core/annotsv/annotsv/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://lbgi.fr/AnnotSV/"
       documentation: "https://lbgi.fr/AnnotSV/"
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
-      licence: "GPL-3.0"
+      licence: ["GPL-3.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/annotsv/installannotations/meta.yml b/modules/nf-core/annotsv/installannotations/meta.yml
index 18a4708bc73..a04c4f1d7fe 100644
--- a/modules/nf-core/annotsv/installannotations/meta.yml
+++ b/modules/nf-core/annotsv/installannotations/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://lbgi.fr/AnnotSV/"
       documentation: "https://lbgi.fr/AnnotSV/"
       tool_dev_url: "https://github.com/lgmgeo/AnnotSV"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 output:
   - versions:
       type: file
diff --git a/modules/nf-core/antismash/antismashlite/meta.yml b/modules/nf-core/antismash/antismashlite/meta.yml
index 2c9ca7f15c4..21f506bd846 100644
--- a/modules/nf-core/antismash/antismashlite/meta.yml
+++ b/modules/nf-core/antismash/antismashlite/meta.yml
@@ -22,7 +22,7 @@ tools:
       documentation: "https://docs.antismash.secondarymetabolites.org"
       tool_dev_url: "https://github.com/antismash/antismash"
       doi: "10.1093/nar/gkab335"
-      licence: "['AGPL v3']"
+      licence: ["AGPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/arcashla/extract/meta.yml b/modules/nf-core/arcashla/extract/meta.yml
index 3575e782051..6a85aad0f79 100644
--- a/modules/nf-core/arcashla/extract/meta.yml
+++ b/modules/nf-core/arcashla/extract/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/RabadanLab/arcasHLA"
       tool_dev_url: "https://github.com/RabadanLab/arcasHLA"
       doi: "10.1093/bioinformatics/btz474"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ariba/getref/meta.yml b/modules/nf-core/ariba/getref/meta.yml
index 38e56e15acc..30087c9529f 100644
--- a/modules/nf-core/ariba/getref/meta.yml
+++ b/modules/nf-core/ariba/getref/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://sanger-pathogens.github.io/ariba/"
       tool_dev_url: "https://github.com/sanger-pathogens/ariba"
       doi: "10.1099/mgen.0.000131"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - db_name:
       type: string
diff --git a/modules/nf-core/art/illumina/meta.yml b/modules/nf-core/art/illumina/meta.yml
index 6e5c9893a7c..5c9b18973fd 100644
--- a/modules/nf-core/art/illumina/meta.yml
+++ b/modules/nf-core/art/illumina/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. "
       homepage: "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm"
       doi: "10.1093/bioinformatics/btr708"
-      licence: "GPL version 3 license"
+      licence: ["GPL version 3 license"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/assemblyscan/meta.yml b/modules/nf-core/assemblyscan/meta.yml
index 9ff7e3f185c..0860123c6e0 100644
--- a/modules/nf-core/assemblyscan/meta.yml
+++ b/modules/nf-core/assemblyscan/meta.yml
@@ -3,6 +3,7 @@ description: Assembly summary statistics in JSON format
 keywords:
   - assembly
   - statistics
+  - summary statistics
 tools:
   - assemblyscan:
       description: Assembly summary statistics in JSON format
diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml
index aecbb13d162..be4ff3ed519 100644
--- a/modules/nf-core/ataqv/mkarv/meta.yml
+++ b/modules/nf-core/ataqv/mkarv/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
       documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
       tool_dev_url: "https://github.com/ParkerLab/ataqv"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - json:
       type: file
diff --git a/modules/nf-core/atlas/call/meta.yml b/modules/nf-core/atlas/call/meta.yml
index 9b1142bdd94..46329f87254 100644
--- a/modules/nf-core/atlas/call/meta.yml
+++ b/modules/nf-core/atlas/call/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -48,7 +48,7 @@ input:
       description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
       pattern: "*.{txt.tsv}"
   - method:
-      type: character
+      type: string
       description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
       pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase"
 output:
diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml
index 7b11d718e48..ed2ec3691ba 100644
--- a/modules/nf-core/atlas/pmd/meta.yml
+++ b/modules/nf-core/atlas/pmd/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/atlas/recal/meta.yml b/modules/nf-core/atlas/recal/meta.yml
index 886e93cb4e6..a629daccaa1 100644
--- a/modules/nf-core/atlas/recal/meta.yml
+++ b/modules/nf-core/atlas/recal/meta.yml
@@ -1,15 +1,16 @@
 name: "atlas_recal"
 description: gives an estimation of the sequencing bias based on known invariant sites
 keywords:
-  - sequencing_bias
+  - sequencing bias
   - ATLAS
+  - invariant sites
 tools:
   - "atlas":
       description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
       homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml
index fc6289c78da..228bb3df107 100644
--- a/modules/nf-core/atlas/splitmerge/meta.yml
+++ b/modules/nf-core/atlas/splitmerge/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
       tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
       doi: "10.1101/105346"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml
index 10aa5366974..3a530cc07a2 100644
--- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml
+++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml
@@ -3,13 +3,14 @@ description: Generate tables of feature metadata from GTF files
 keywords:
   - gtf
   - annotation
+  - feature
 tools:
   - "atlasgeneannotationmanipulation":
       description: "Scripts for manipulating gene annotation"
       homepage: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation"
       documentation: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation"
       tool_dev_url: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/authentict/deam2cont/meta.yml b/modules/nf-core/authentict/deam2cont/meta.yml
index 097f6079aa4..0c05fbc4633 100644
--- a/modules/nf-core/authentict/deam2cont/meta.yml
+++ b/modules/nf-core/authentict/deam2cont/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/StephanePeyregne/AuthentiCT"
       tool_dev_url: "https://github.com/StephanePeyregne/AuthentiCT"
       doi: "10.1186/s13059-020-02123-y"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/bamaligncleaner/meta.yml b/modules/nf-core/bamaligncleaner/meta.yml
index f7f9548c434..078d6fe92a3 100644
--- a/modules/nf-core/bamaligncleaner/meta.yml
+++ b/modules/nf-core/bamaligncleaner/meta.yml
@@ -2,6 +2,8 @@ name: bamaligncleaner
 description: removes unused references from header of sorted BAM/CRAM files.
 keywords:
   - bam
+  - header
+  - unused reference
 tools:
   - bamaligncleaner:
       description: Removes unaligned references in aligned BAM alignment file
diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml
index 3aaf407abb1..0e6c5244338 100644
--- a/modules/nf-core/barrnap/meta.yml
+++ b/modules/nf-core/barrnap/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/tseemann/barrnap"
       documentation: "https://github.com/tseemann/barrnap"
       tool_dev_url: "https://github.com/tseemann/barrnap"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml
index 077ae029120..6a43b94d70b 100644
--- a/modules/nf-core/basicpy/meta.yml
+++ b/modules/nf-core/basicpy/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://basicpy.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/peng-lab/BaSiCPy"
       doi: 10.1038/ncomms14836
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/bbmap/align/meta.yml b/modules/nf-core/bbmap/align/meta.yml
index a0bddba4010..3be243ff040 100644
--- a/modules/nf-core/bbmap/align/meta.yml
+++ b/modules/nf-core/bbmap/align/meta.yml
@@ -10,8 +10,8 @@ keywords:
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
       licence: ["UC-LBL license (see package)"]
 input:
   - meta:
diff --git a/modules/nf-core/bbmap/bbduk/meta.yml b/modules/nf-core/bbmap/bbduk/meta.yml
index 9a1f0562860..d60ea7145a5 100644
--- a/modules/nf-core/bbmap/bbduk/meta.yml
+++ b/modules/nf-core/bbmap/bbduk/meta.yml
@@ -8,8 +8,8 @@ keywords:
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
       licence: ["UC-LBL license (see package)"]
 input:
   - meta:
diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml
index 6c8426f88f1..74dff3816d7 100644
--- a/modules/nf-core/bbmap/bbnorm/meta.yml
+++ b/modules/nf-core/bbmap/bbnorm/meta.yml
@@ -7,10 +7,9 @@ keywords:
 tools:
   - bbmap:
       description: "BBMap is a short read aligner, as well as various other bioinformatic tools."
-      homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
-      documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
-      tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/"
-      licence: "BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"
+      homepage: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
+      documentation: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/"
+      licence: ["BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
index f4e0a5ed58e..4b322593e22 100644
--- a/modules/nf-core/bbmap/bbsplit/meta.yml
+++ b/modules/nf-core/bbmap/bbsplit/meta.yml
@@ -9,8 +9,8 @@ keywords:
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
       licence: ["UC-LBL license (see package)"]
 input:
   - meta:
diff --git a/modules/nf-core/bbmap/index/meta.yml b/modules/nf-core/bbmap/index/meta.yml
index 7e1cbc9f81d..79b65a02766 100644
--- a/modules/nf-core/bbmap/index/meta.yml
+++ b/modules/nf-core/bbmap/index/meta.yml
@@ -7,12 +7,12 @@ keywords:
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
       licence: ["UC-LBL license (see package)"]
 input:
   - fasta:
-      type: fasta
+      type: file
       description: fasta formatted file with nucleotide sequences
       pattern: "*.{fna,fa,fasta}"
 output:
diff --git a/modules/nf-core/bbmap/pileup/meta.yml b/modules/nf-core/bbmap/pileup/meta.yml
index 5620fd803a8..fe7c006f1f5 100644
--- a/modules/nf-core/bbmap/pileup/meta.yml
+++ b/modules/nf-core/bbmap/pileup/meta.yml
@@ -7,8 +7,8 @@ keywords:
 tools:
   - bbmap:
       description: BBMap is a short read aligner, as well as various other bioinformatic tools.
-      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
-      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
+      homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
+      documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide//
       tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
       licence: ["UC-LBL license (see package)"]
 input:
diff --git a/modules/nf-core/bbmap/sendsketch/meta.yml b/modules/nf-core/bbmap/sendsketch/meta.yml
index 38a5fb3fe6a..fcdfd8b0b43 100644
--- a/modules/nf-core/bbmap/sendsketch/meta.yml
+++ b/modules/nf-core/bbmap/sendsketch/meta.yml
@@ -10,9 +10,9 @@ keywords:
 tools:
   - "bbmap":
       description: "BBMap is a short read aligner, as well as various other bioinformatic tools."
-      homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
-      documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/"
-      licence: "['UC-LBL license (see package)']"
+      homepage: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
+      documentation: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
+      licence: ["UC-LBL license (see package)"]
 input:
   - meta:
       type: map
@@ -34,7 +34,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - hits:
-      type: txt
+      type: file
       description: .txt file containing hits from a query seuqnce to various reference sequences output
       pattern: "*.{txt}"
 authors:
diff --git a/modules/nf-core/bcl2fastq/meta.yml b/modules/nf-core/bcl2fastq/meta.yml
index 34d7762fae0..42c50573133 100644
--- a/modules/nf-core/bcl2fastq/meta.yml
+++ b/modules/nf-core/bcl2fastq/meta.yml
@@ -7,9 +7,8 @@ keywords:
 tools:
   - "bcl2fastq":
       description: "Demultiplex Illumina BCL files"
-      homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software"
       documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf"
-      licence: "ILLUMINA"
+      licence: ["ILLUMINA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/beagle5/beagle/meta.yml b/modules/nf-core/beagle5/beagle/meta.yml
index 03b50869270..cf47f91f5c5 100644
--- a/modules/nf-core/beagle5/beagle/meta.yml
+++ b/modules/nf-core/beagle5/beagle/meta.yml
@@ -3,13 +3,15 @@ description: Beagle v5.2 is a software package for phasing genotypes and for imp
 keywords:
   - phasing
   - imputation
+  - genotypes
+  - ungenotyped markers
 tools:
   - "beagle5":
       description: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers."
       homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html"
       documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf"
       doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index c9d0011182b..7af01582195 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://github.com/lh3/bioawk"
       documentation: "https://github.com/lh3/bioawk"
       tool_dev_url: "https://github.com/lh3/bioawk"
-      licence: "['Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)']"
+      licence: ["Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/biobambam/bammerge/meta.yml b/modules/nf-core/biobambam/bammerge/meta.yml
index 8be274e161a..1044767cec3 100644
--- a/modules/nf-core/biobambam/bammerge/meta.yml
+++ b/modules/nf-core/biobambam/bammerge/meta.yml
@@ -3,6 +3,7 @@ description: Merge a list of sorted bam files
 keywords:
   - merge
   - bam
+  - biobambam
 tools:
   - biobambam:
       description: |
diff --git a/modules/nf-core/biohansel/meta.yml b/modules/nf-core/biohansel/meta.yml
index e3ffc82e679..41aa8b6ee8e 100644
--- a/modules/nf-core/biohansel/meta.yml
+++ b/modules/nf-core/biohansel/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/phac-nml/biohansel"
       tool_dev_url: "https://github.com/phac-nml/biohansel"
       doi: "10.1101/2020.01.10.902056"
-      licence: "['Apache-2.0 license']"
+      licence: ["Apache-2.0 license"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/biscuit/bsconv/meta.yml b/modules/nf-core/biscuit/bsconv/meta.yml
index e0919db3197..0db30255dfc 100644
--- a/modules/nf-core/biscuit/bsconv/meta.yml
+++ b/modules/nf-core/biscuit/bsconv/meta.yml
@@ -29,7 +29,7 @@ input:
       type: file
       description: BAM file index
   - index:
-      type: dir
+      type: directory
       description: Biscuit genome index directory (generated with 'biscuit index')
       pattern: "BiscuitIndex"
 output:
diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml
index e9d6bde08c8..db05862ca01 100644
--- a/modules/nf-core/bismark/coverage2cytosine/meta.yml
+++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml
@@ -31,7 +31,7 @@ input:
       description: |
         A file containing methylation calls per position, in the format produced by bismark_methylation_extractor.
   - index:
-      type: dir
+      type: directory
       description: Bismark genome index directory
       pattern: "BismarkIndex"
 output:
diff --git a/modules/nf-core/blast/blastp/meta.yml b/modules/nf-core/blast/blastp/meta.yml
index 2d1a2114441..443c9b7cb28 100644
--- a/modules/nf-core/blast/blastp/meta.yml
+++ b/modules/nf-core/blast/blastp/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
       documentation: "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs"
       doi: "10.1016/S0022-2836(05)80360-2"
-      licence: "['US-Government-Work']"
+      licence: ["US-Government-Work"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml
index f03142d9b36..25deca1aea3 100644
--- a/modules/nf-core/blat/meta.yml
+++ b/modules/nf-core/blat/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://kentinformatics.com/"
       documentation: "https://kentinformatics.com/documentation"
       doi: "10.1101/gr.229202"
-      licence: "['Free for academic, nonprofit and personal use']"
+      licence: ["Free for academic, nonprofit and personal use"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml
index 0b0b4f95d07..9df893dc191 100644
--- a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml
+++ b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml
@@ -2,6 +2,8 @@ name: "bracken_combinebrackenoutputs"
 description: Combine output of metagenomic samples analyzed by bracken.
 keywords:
   - sort
+  - bracken
+  - metagenomics
 tools:
   - "bracken":
       description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml
index df84d237c54..615cef06731 100644
--- a/modules/nf-core/cadd/meta.yml
+++ b/modules/nf-core/cadd/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/kircherlab/CADD-scripts/blob/master/README.md"
       tool_dev_url: "https://github.com/kircherlab/CADD-scripts/"
       doi: "10.1093/nar/gky1016"
-      licence: "['Restricted. Free for non-commercial users.']"
+      licence: ["Restricted. Free for non-commercial users."]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/canu/meta.yml b/modules/nf-core/canu/meta.yml
index 2feed43fa7a..afcaa55b9e9 100644
--- a/modules/nf-core/canu/meta.yml
+++ b/modules/nf-core/canu/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://canu.readthedocs.io/en/latest/tutorial.html"
       tool_dev_url: "https://github.com/marbl/canu"
       doi: "10.1101/gr.215087.116"
-      licence: "['GPL v2 and others']"
+      licence: ["GPL v2 and others"]
 input:
   - meta:
       type: map
@@ -24,11 +24,11 @@ input:
       description: fasta/fastq file
       pattern: "*.{fasta,fastq}"
   - mode:
-      type: value
+      type: string
       description: Canu mode depending on the input data (source and error rate)
       pattern: "-pacbio|-nanopore|-pacbio-hifi"
   - genomesize:
-      type: value
+      type: string
       description: An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g
       pattern: "<number>[g|m|k]"
 output:
diff --git a/modules/nf-core/cdhit/cdhitest/meta.yml b/modules/nf-core/cdhit/cdhitest/meta.yml
index 4c850aa02e2..c6b2dfc82b0 100644
--- a/modules/nf-core/cdhit/cdhitest/meta.yml
+++ b/modules/nf-core/cdhit/cdhitest/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/weizhongli/cdhit/wiki"
       tool_dev_url: "https://github.com/weizhongli/cdhit"
       doi: "10.1093/bioinformatics/btl158"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
index c1f4259a996..3d2266b37df 100644
--- a/modules/nf-core/cellranger/count/meta.yml
+++ b/modules/nf-core/cellranger/count/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cellranger/mkfastq/meta.yml b/modules/nf-core/cellranger/mkfastq/meta.yml
index 18d9e1d1f1f..4c7e9a5c003 100644
--- a/modules/nf-core/cellranger/mkfastq/meta.yml
+++ b/modules/nf-core/cellranger/mkfastq/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - bcl:
       type: file
diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml
index a01e2830da5..a5b988a617a 100644
--- a/modules/nf-core/cellranger/mkgtf/meta.yml
+++ b/modules/nf-core/cellranger/mkgtf/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - gtf:
       type: file
diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml
index 4cd9091cb98..39272b8bf96 100644
--- a/modules/nf-core/cellranger/mkref/meta.yml
+++ b/modules/nf-core/cellranger/mkref/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/cellranger/multi/meta.yml b/modules/nf-core/cellranger/multi/meta.yml
index 5ac3ebdbb87..0f5567e3790 100644
--- a/modules/nf-core/cellranger/multi/meta.yml
+++ b/modules/nf-core/cellranger/multi/meta.yml
@@ -16,7 +16,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp
       tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp
-      licence: [10X Genomics EULA]
+      licence: ["10x Genomics EULA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cellranger/vdj/meta.yml b/modules/nf-core/cellranger/vdj/meta.yml
index ac5caa408f1..2318108f776 100644
--- a/modules/nf-core/cellranger/vdj/meta.yml
+++ b/modules/nf-core/cellranger/vdj/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger
       documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj
       tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cellrangeratac/count/meta.yml b/modules/nf-core/cellrangeratac/count/meta.yml
index dc422ad0eda..2bdef7f60d9 100644
--- a/modules/nf-core/cellrangeratac/count/meta.yml
+++ b/modules/nf-core/cellrangeratac/count/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cellrangeratac/mkfastq/meta.yml b/modules/nf-core/cellrangeratac/mkfastq/meta.yml
index 46b01ba7082..fcee368d1ac 100644
--- a/modules/nf-core/cellrangeratac/mkfastq/meta.yml
+++ b/modules/nf-core/cellrangeratac/mkfastq/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - bcl:
       type: file
diff --git a/modules/nf-core/cellrangeratac/mkref/meta.yml b/modules/nf-core/cellrangeratac/mkref/meta.yml
index e1d755c402a..4baed308375 100644
--- a/modules/nf-core/cellrangeratac/mkref/meta.yml
+++ b/modules/nf-core/cellrangeratac/mkref/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
       tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
-      licence: 10x Genomics EULA
+      licence: ["10x Genomics EULA"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/centrifuge/kreport/meta.yml b/modules/nf-core/centrifuge/kreport/meta.yml
index 5641152b675..d27928b7f28 100644
--- a/modules/nf-core/centrifuge/kreport/meta.yml
+++ b/modules/nf-core/centrifuge/kreport/meta.yml
@@ -3,6 +3,7 @@ description: Creates Kraken-style reports from centrifuge out files
 keywords:
   - classify
   - metagenomics
+  - centrifuge
   - fastq
   - db
   - report
diff --git a/modules/nf-core/chopper/meta.yml b/modules/nf-core/chopper/meta.yml
index 34d19abba2f..9d8093d66bc 100644
--- a/modules/nf-core/chopper/meta.yml
+++ b/modules/nf-core/chopper/meta.yml
@@ -17,7 +17,7 @@ tools:
       documentation: "https://github.com/wdecoster/chopper"
       tool_dev_url: "https://github.com/wdecoster/chopper"
       doi: "10.1093/bioinformatics/bty149"
-      licence: "['MIT']"
+      licence: ["MIT"]
       args_id: "$args2"
   - "gzip":
       description: "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77)."
diff --git a/modules/nf-core/circexplorer2/annotate/meta.yml b/modules/nf-core/circexplorer2/annotate/meta.yml
index e11df81c2fc..b33d966598a 100644
--- a/modules/nf-core/circexplorer2/annotate/meta.yml
+++ b/modules/nf-core/circexplorer2/annotate/meta.yml
@@ -3,13 +3,14 @@ description: Annotate circRNAs detected in the output from CIRCexplorer2 parse
 keywords:
   - circrna
   - annotate
+  - circexplorer2
 tools:
   - "circexplorer2":
       description: "Circular RNA analysis toolkits"
       homepage: "https://github.com/YangLab/CIRCexplorer2/"
       documentation: "https://circexplorer2.readthedocs.io/en/latest/"
       doi: "10.1101/gr.202895.115"
-      licence: "['MIT License']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml
index ef3ebf85643..83e6e9d35b4 100644
--- a/modules/nf-core/circexplorer2/parse/meta.yml
+++ b/modules/nf-core/circexplorer2/parse/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/YangLab/CIRCexplorer2/"
       documentation: "https://circexplorer2.readthedocs.io/en/latest/"
       doi: "10.1101/gr.202895.115"
-      licence: "['MIT License']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/clippy/meta.yml b/modules/nf-core/clippy/meta.yml
index 547bf39bc0e..cdb9f00b843 100644
--- a/modules/nf-core/clippy/meta.yml
+++ b/modules/nf-core/clippy/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/ulelab/clippy"
       tool_dev_url: "https://github.com/ulelab/clippy"
       doi: "10.7554/eLife.84034"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml
index 2afbacdea1d..627b76b993d 100644
--- a/modules/nf-core/cnvnator/cnvnator/meta.yml
+++ b/modules/nf-core/cnvnator/cnvnator/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/abyzovlab/CNVnator"
       documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md"
       tool_dev_url: "https://github.com/abyzovlab/CNVnator"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cnvnator/convert2vcf/meta.yml b/modules/nf-core/cnvnator/convert2vcf/meta.yml
index 8e8c80064c8..b7d269e0480 100644
--- a/modules/nf-core/cnvnator/convert2vcf/meta.yml
+++ b/modules/nf-core/cnvnator/convert2vcf/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/abyzovlab/CNVnator"
       documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md"
       tool_dev_url: "https://github.com/abyzovlab/CNVnator"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cnvpytor/callcnvs/meta.yml b/modules/nf-core/cnvpytor/callcnvs/meta.yml
index 211cb6079cb..2286d511910 100644
--- a/modules/nf-core/cnvpytor/callcnvs/meta.yml
+++ b/modules/nf-core/cnvpytor/callcnvs/meta.yml
@@ -2,6 +2,9 @@ name: cnvpytor_callcnvs
 description: command line tool for calling CNVs in whole genome sequencing data
 keywords:
   - CNV calling
+  - CNVpytor
+  - WGS
+  - whole genome sequencing
 tools:
   - cnvpytor:
       description: calling CNVs using read depth
diff --git a/modules/nf-core/cnvpytor/histogram/meta.yml b/modules/nf-core/cnvpytor/histogram/meta.yml
index 69f0c49396d..e8fcedd47f6 100644
--- a/modules/nf-core/cnvpytor/histogram/meta.yml
+++ b/modules/nf-core/cnvpytor/histogram/meta.yml
@@ -3,6 +3,7 @@ description: calculates read depth histograms
 keywords:
   - cnv calling
   - histogram
+  - read depth
 tools:
   - cnvpytor:
       description: calling CNVs using read depth
diff --git a/modules/nf-core/cnvpytor/importreaddepth/meta.yml b/modules/nf-core/cnvpytor/importreaddepth/meta.yml
index 009fad37013..0780b624a14 100644
--- a/modules/nf-core/cnvpytor/importreaddepth/meta.yml
+++ b/modules/nf-core/cnvpytor/importreaddepth/meta.yml
@@ -3,6 +3,7 @@ description: command line tool for CNV/CNA analysis. This step imports the read
 keywords:
   - read depth
   - cnv calling
+  - pytor
 tools:
   - cnvpytor -rd:
       description: calling CNVs using read depth
diff --git a/modules/nf-core/cnvpytor/partition/meta.yml b/modules/nf-core/cnvpytor/partition/meta.yml
index 5775fa76de2..c9a04d30516 100644
--- a/modules/nf-core/cnvpytor/partition/meta.yml
+++ b/modules/nf-core/cnvpytor/partition/meta.yml
@@ -3,6 +3,7 @@ description: partitioning read depth histograms
 keywords:
   - cnv calling
   - partition histograms
+  - read depth
 tools:
   - cnvpytor:
       description: calling CNVs using read depth
diff --git a/modules/nf-core/cnvpytor/view/meta.yml b/modules/nf-core/cnvpytor/view/meta.yml
index 64eaddbd2ce..f37e806c7f6 100644
--- a/modules/nf-core/cnvpytor/view/meta.yml
+++ b/modules/nf-core/cnvpytor/view/meta.yml
@@ -2,6 +2,8 @@ name: cnvpytor_view
 description: view function to generate vcfs
 keywords:
   - cnv calling
+  - vcf
+  - copy number variation
 tools:
   - cnvpytor:
       description: calling CNVs using read depth
diff --git a/modules/nf-core/concoct/concoct/meta.yml b/modules/nf-core/concoct/concoct/meta.yml
index b815705a128..cd7afba29d5 100644
--- a/modules/nf-core/concoct/concoct/meta.yml
+++ b/modules/nf-core/concoct/concoct/meta.yml
@@ -17,7 +17,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/concoct/concoctcoveragetable/meta.yml b/modules/nf-core/concoct/concoctcoveragetable/meta.yml
index c6413c7434e..26b9793c9c8 100644
--- a/modules/nf-core/concoct/concoctcoveragetable/meta.yml
+++ b/modules/nf-core/concoct/concoctcoveragetable/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/concoct/cutupfasta/meta.yml b/modules/nf-core/concoct/cutupfasta/meta.yml
index 5d4a8a2d064..44a28723300 100644
--- a/modules/nf-core/concoct/cutupfasta/meta.yml
+++ b/modules/nf-core/concoct/cutupfasta/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/concoct/extractfastabins/meta.yml b/modules/nf-core/concoct/extractfastabins/meta.yml
index 39309b01037..a9ac00a304c 100644
--- a/modules/nf-core/concoct/extractfastabins/meta.yml
+++ b/modules/nf-core/concoct/extractfastabins/meta.yml
@@ -17,7 +17,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/concoct/mergecutupclustering/meta.yml b/modules/nf-core/concoct/mergecutupclustering/meta.yml
index 88b39f91ff6..e34a423c22b 100644
--- a/modules/nf-core/concoct/mergecutupclustering/meta.yml
+++ b/modules/nf-core/concoct/mergecutupclustering/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://concoct.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/BinPro/CONCOCT"
       doi: "10.1038/nmeth.3103"
-      licence: "['FreeBSD']"
+      licence: ["FreeBSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml
index cbff776e19e..34b2f911c80 100644
--- a/modules/nf-core/coreograph/meta.yml
+++ b/modules/nf-core/coreograph/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html"
       tool_dev_url: "https://github.com/HMS-IDAC/UNetCoreograph"
       doi: 10.1038/s41592-021-01308-y
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   - image:
       type: file
diff --git a/modules/nf-core/crisprcleanr/normalize/meta.yml b/modules/nf-core/crisprcleanr/normalize/meta.yml
index e76a414fa33..f20492fd744 100644
--- a/modules/nf-core/crisprcleanr/normalize/meta.yml
+++ b/modules/nf-core/crisprcleanr/normalize/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf"
       tool_dev_url: "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0"
       doi: "10.1186/s12864-018-4989-y"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/crumble/meta.yml b/modules/nf-core/crumble/meta.yml
index 59d7a79643f..66665f127f6 100644
--- a/modules/nf-core/crumble/meta.yml
+++ b/modules/nf-core/crumble/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/jkbonfield/crumble"
       tool_dev_url: "https://github.com/jkbonfield/crumble"
       doi: "10.1093/bioinformatics/bty608"
-      licence: "['multiple BSD style licenses']"
+      licence: ["multiple BSD style licenses"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/cutesv/meta.yml b/modules/nf-core/cutesv/meta.yml
index 9054101f125..c92bcdab5a2 100644
--- a/modules/nf-core/cutesv/meta.yml
+++ b/modules/nf-core/cutesv/meta.yml
@@ -1,8 +1,9 @@
 name: cutesv
 description: structural-variant calling with cutesv
 keywords:
-  - cutesv
   - structural-variant calling
+  - clustering and refinement
+  - signatures
 tools:
   - cutesv:
       description: a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.
diff --git a/modules/nf-core/damageprofiler/meta.yml b/modules/nf-core/damageprofiler/meta.yml
index 8a9307f1a25..7cf1a4a5146 100644
--- a/modules/nf-core/damageprofiler/meta.yml
+++ b/modules/nf-core/damageprofiler/meta.yml
@@ -47,7 +47,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - results:
-      type: dir
+      type: directory
       description: DamageProfiler results directory
       pattern: "*/*"
 authors:
diff --git a/modules/nf-core/dastool/fastatocontig2bin/meta.yml b/modules/nf-core/dastool/fastatocontig2bin/meta.yml
index 8ab64d65ee5..bbecfd27ef7 100644
--- a/modules/nf-core/dastool/fastatocontig2bin/meta.yml
+++ b/modules/nf-core/dastool/fastatocontig2bin/meta.yml
@@ -31,7 +31,7 @@ input:
       description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins
       pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
   - extension:
-      type: val
+      type: string
       description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input.
 output:
   - meta:
diff --git a/modules/nf-core/dastool/scaffolds2bin/meta.yml b/modules/nf-core/dastool/scaffolds2bin/meta.yml
index f439f41f47d..f57c50ab017 100644
--- a/modules/nf-core/dastool/scaffolds2bin/meta.yml
+++ b/modules/nf-core/dastool/scaffolds2bin/meta.yml
@@ -31,7 +31,7 @@ input:
       description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins
       pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
   - extension:
-      type: val
+      type: string
       description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input.
 output:
   - meta:
diff --git a/modules/nf-core/deeptools/multibamsummary/meta.yml b/modules/nf-core/deeptools/multibamsummary/meta.yml
index 30c2f235083..f355b311515 100644
--- a/modules/nf-core/deeptools/multibamsummary/meta.yml
+++ b/modules/nf-core/deeptools/multibamsummary/meta.yml
@@ -3,6 +3,7 @@ description: Computes read coverage for genomic regions (bins) across the entire
 keywords:
   - bam
   - coverage
+  - read coverage
 tools:
   - deeptools:
       description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
diff --git a/modules/nf-core/deeptools/plotpca/meta.yml b/modules/nf-core/deeptools/plotpca/meta.yml
index 9035f694e88..b9ffa3e60fe 100644
--- a/modules/nf-core/deeptools/plotpca/meta.yml
+++ b/modules/nf-core/deeptools/plotpca/meta.yml
@@ -3,6 +3,9 @@ description: Generates principal component analysis (PCA) plot using a compresse
 keywords:
   - PCA
   - matrix
+  - deeptools
+  - mutlibamsummary
+  - multibigwigsummary
 tools:
   - deeptools:
       description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml
index c82cf7545ed..c5c0677df55 100644
--- a/modules/nf-core/duphold/meta.yml
+++ b/modules/nf-core/duphold/meta.yml
@@ -2,6 +2,8 @@ name: "duphold"
 description: SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content.
 keywords:
   - sort
+  - SV calling
+  - depth information
 tools:
   - "duphold":
       description: "SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls."
@@ -9,7 +11,7 @@ tools:
       documentation: "https://github.com/brentp/duphold"
       tool_dev_url: "https://github.com/brentp/duphold"
       doi: "10.1093/gigascience/giz040"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/eido/convert/meta.yml b/modules/nf-core/eido/convert/meta.yml
index c340701491b..9c84140154f 100644
--- a/modules/nf-core/eido/convert/meta.yml
+++ b/modules/nf-core/eido/convert/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "http://eido.databio.org/en/latest/"
       documentation: "http://eido.databio.org/en/latest/"
       doi: "10.1093/gigascience/giab077"
-      licence: "BSD-2-Clause"
+      licence: ["BSD-2-Clause"]
 input:
   - samplesheet:
       type: file
diff --git a/modules/nf-core/eido/validate/meta.yml b/modules/nf-core/eido/validate/meta.yml
index f585a3f58a5..3d895af2903 100644
--- a/modules/nf-core/eido/validate/meta.yml
+++ b/modules/nf-core/eido/validate/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "http://eido.databio.org/en/latest/"
       documentation: "http://eido.databio.org/en/latest/"
       doi: "10.1093/gigascience/giab077"
-      licence: "BSD-2-Clause"
+      licence: ["BSD-2-Clause"]
 input:
   - samplesheet:
       type: file
diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml
index cf48d5ce2e4..bb4c7f84b7f 100644
--- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml
+++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml
@@ -11,7 +11,7 @@ tools:
       description: "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases."
       documentation: "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md"
       tool_dev_url: "https://github.com/TCLamnidis/EigenStratDatabaseTools"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml
index 4876c3bce3e..7f7ebb2a382 100644
--- a/modules/nf-core/elprep/filter/meta.yml
+++ b/modules/nf-core/elprep/filter/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/ExaScience/elprep"
       tool_dev_url: "https://github.com/ExaScience/elprep"
       doi: "10.1371/journal.pone.0244471"
-      licence: "['AGPL v3']"
+      licence: ["AGPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/elprep/merge/meta.yml b/modules/nf-core/elprep/merge/meta.yml
index 6dd8ebacfba..ec7ec6de292 100644
--- a/modules/nf-core/elprep/merge/meta.yml
+++ b/modules/nf-core/elprep/merge/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/ExaScience/elprep"
       tool_dev_url: "https://github.com/ExaScience/elprep"
       doi: "10.1371/journal.pone.0244471"
-      licence: "['AGPL v3']"
+      licence: ["AGPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/elprep/split/meta.yml b/modules/nf-core/elprep/split/meta.yml
index 040e4815497..1c618fcf717 100644
--- a/modules/nf-core/elprep/split/meta.yml
+++ b/modules/nf-core/elprep/split/meta.yml
@@ -3,6 +3,7 @@ description: Split bam file into manageable chunks
 keywords:
   - bam
   - split by chromosome
+  - elPrep
 tools:
   - "elprep":
       description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
@@ -10,7 +11,7 @@ tools:
       documentation: "https://github.com/ExaScience/elprep"
       tool_dev_url: "https://github.com/ExaScience/elprep"
       doi: "10.1371/journal.pone.0244471"
-      licence: "['AGPL v3']"
+      licence: ["AGPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/endorspy/meta.yml b/modules/nf-core/endorspy/meta.yml
index d1a363e01f4..4578998425b 100644
--- a/modules/nf-core/endorspy/meta.yml
+++ b/modules/nf-core/endorspy/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/aidaanva/endorS.py"
       tool_dev_url: "https://github.com/aidaanva/endorS.py"
       doi: "10.7717/peerj.10947"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/entrezdirect/esummary/meta.yml b/modules/nf-core/entrezdirect/esummary/meta.yml
index f82eaafa898..8f0dbd589e5 100644
--- a/modules/nf-core/entrezdirect/esummary/meta.yml
+++ b/modules/nf-core/entrezdirect/esummary/meta.yml
@@ -28,10 +28,10 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - database:
-      type: value
+      type: string
       description: Value must be a valid Entrez database name ('assembly', etc).
   - uid:
-      type: value
+      type: string
       description: Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file
   - uids_file:
       type: file
diff --git a/modules/nf-core/epang/place/meta.yml b/modules/nf-core/epang/place/meta.yml
index 7d31a34972e..be90ceabfc4 100644
--- a/modules/nf-core/epang/place/meta.yml
+++ b/modules/nf-core/epang/place/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
       tool_dev_url: "https://github.com/Pbdas/epa-ng"
       doi: "10.1093/sysbio/syy054"
-      licence: "['GNU Affero General Public License v3.0']"
+      licence: ["GNU Affero General Public License v3.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/epang/split/meta.yml b/modules/nf-core/epang/split/meta.yml
index 5af4234f0ae..21cb81ae217 100644
--- a/modules/nf-core/epang/split/meta.yml
+++ b/modules/nf-core/epang/split/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
       tool_dev_url: "https://github.com/Pbdas/epa-ng"
       doi: "10.1093/sysbio/syy054"
-      licence: "['GNU Affero General Public License v3.0']"
+      licence: ["GNU Affero General Public License v3.0"]
 input:
   # Only when we have meta
   - meta:
diff --git a/modules/nf-core/estsfs/meta.yml b/modules/nf-core/estsfs/meta.yml
index cae1988afcc..9d3d0d80da1 100644
--- a/modules/nf-core/estsfs/meta.yml
+++ b/modules/nf-core/estsfs/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://sourceforge.net/projects/est-usfs/"
       tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz"
       doi: "10.1534/genetics.118.301120"
-      licence: "['Free for Academic Use']"
+      licence: ["Free for Academic Use"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/expansionhunterdenovo/merge/meta.yml b/modules/nf-core/expansionhunterdenovo/merge/meta.yml
index a0eb8e2d6df..a7aa59fb405 100644
--- a/modules/nf-core/expansionhunterdenovo/merge/meta.yml
+++ b/modules/nf-core/expansionhunterdenovo/merge/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/Illumina/ExpansionHunterDenovo"
       documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md"
       tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/expansionhunterdenovo/profile/meta.yml b/modules/nf-core/expansionhunterdenovo/profile/meta.yml
index d10fdd1e7da..68fac10a2a5 100644
--- a/modules/nf-core/expansionhunterdenovo/profile/meta.yml
+++ b/modules/nf-core/expansionhunterdenovo/profile/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://github.com/Illumina/ExpansionHunterDenovo"
       documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md"
       tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fastawindows/meta.yml b/modules/nf-core/fastawindows/meta.yml
index 494cc1b6afd..87f1d8b7dcf 100644
--- a/modules/nf-core/fastawindows/meta.yml
+++ b/modules/nf-core/fastawindows/meta.yml
@@ -9,7 +9,7 @@ tools:
   - "fastawindows":
       description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows"
       homepage: "https://github.com/tolkit/fasta_windows"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fastk/fastk/meta.yml b/modules/nf-core/fastk/fastk/meta.yml
index 7c7f4260ce5..8872c17035a 100644
--- a/modules/nf-core/fastk/fastk/meta.yml
+++ b/modules/nf-core/fastk/fastk/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "A fast K-mer counter for high-fidelity shotgun datasets"
       homepage: "https://github.com/thegenemyers/FASTK"
       tool_dev_url: "https://github.com/thegenemyers/FASTK"
-      licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE"
+      licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fastk/histex/meta.yml b/modules/nf-core/fastk/histex/meta.yml
index e7497ffa81b..00a6c5a177e 100644
--- a/modules/nf-core/fastk/histex/meta.yml
+++ b/modules/nf-core/fastk/histex/meta.yml
@@ -3,12 +3,14 @@ description: A fast K-mer counter for high-fidelity shotgun datasets
 keywords:
   - k-mer
   - histogram
+  - fastk
+  - shotgun
 tools:
   - "fastk":
       description: "A fast K-mer counter for high-fidelity shotgun datasets"
       homepage: "https://github.com/thegenemyers/FASTK"
       tool_dev_url: "https://github.com/thegenemyers/FASTK"
-      licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE"
+      licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fastk/merge/meta.yml b/modules/nf-core/fastk/merge/meta.yml
index 60bfa39718c..931e28df842 100644
--- a/modules/nf-core/fastk/merge/meta.yml
+++ b/modules/nf-core/fastk/merge/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: "A fast K-mer counter for high-fidelity shotgun datasets"
       homepage: "https://github.com/thegenemyers/FASTK"
       tool_dev_url: "https://github.com/thegenemyers/FASTK"
-      licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE"
+      licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fasttree/meta.yml b/modules/nf-core/fasttree/meta.yml
index 60fec06dfbf..c3747b16610 100644
--- a/modules/nf-core/fasttree/meta.yml
+++ b/modules/nf-core/fasttree/meta.yml
@@ -3,6 +3,7 @@ description: Produces a Newick format phylogeny from a multiple sequence alignme
 keywords:
   - phylogeny
   - newick
+  - multiple sequence alignment
 tools:
   - fasttree:
       description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
diff --git a/modules/nf-core/fcs/fcsadaptor/meta.yml b/modules/nf-core/fcs/fcsadaptor/meta.yml
index d98c1b0ec98..90c68201d6c 100644
--- a/modules/nf-core/fcs/fcsadaptor/meta.yml
+++ b/modules/nf-core/fcs/fcsadaptor/meta.yml
@@ -17,7 +17,7 @@ tools:
       homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/"
       documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor"
       tool_dev_url: "https://github.com/ncbi/fcs"
-      licence: "United States Government Work"
+      licence: ["United States Government Work"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fcs/fcsgx/meta.yml b/modules/nf-core/fcs/fcsgx/meta.yml
index 2de17874024..8d95189cd6f 100644
--- a/modules/nf-core/fcs/fcsgx/meta.yml
+++ b/modules/nf-core/fcs/fcsgx/meta.yml
@@ -17,7 +17,7 @@ tools:
       homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/"
       documentation: "https://github.com/ncbi/fcs/wiki/FCS-GX"
       tool_dev_url: "https://github.com/ncbi/fcs"
-      licence: "United States Government Work"
+      licence: ["United States Government Work"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ffq/meta.yml b/modules/nf-core/ffq/meta.yml
index f39532fa59c..d5f17873855 100644
--- a/modules/nf-core/ffq/meta.yml
+++ b/modules/nf-core/ffq/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://github.com/pachterlab/ffq#usage
       tool_dev_url: https://github.com/pachterlab/ffq
       doi: "10.1101/2022.05.18.492548"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - ids:
       type: list
diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml
index 6d9e87cb145..1d12f7e147e 100644
--- a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml
+++ b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: http://fulcrumgenomics.github.io/fgbio/
       documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html
       tool_dev_url: https://github.com/fulcrumgenomics/fgbio
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta:
diff --git a/modules/nf-core/fgbio/filterconsensusreads/meta.yml b/modules/nf-core/fgbio/filterconsensusreads/meta.yml
index e7c21c98530..90db0d4ee1c 100644
--- a/modules/nf-core/fgbio/filterconsensusreads/meta.yml
+++ b/modules/nf-core/fgbio/filterconsensusreads/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: http://fulcrumgenomics.github.io/fgbio/
       documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html
       tool_dev_url: https://github.com/fulcrumgenomics/fgbio
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fgbio/zipperbams/meta.yml b/modules/nf-core/fgbio/zipperbams/meta.yml
index 25dbfdb0ec6..ecd1ab176c5 100644
--- a/modules/nf-core/fgbio/zipperbams/meta.yml
+++ b/modules/nf-core/fgbio/zipperbams/meta.yml
@@ -3,6 +3,7 @@ description: FGBIO tool to zip together an unmapped and mapped BAM to transfer m
 keywords:
   - fgbio
   - zipperbams
+  - bam metadata
 tools:
   - fgbio:
       description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
diff --git a/modules/nf-core/flye/meta.yml b/modules/nf-core/flye/meta.yml
index 5c3c816d7b9..4b030d9ec52 100644
--- a/modules/nf-core/flye/meta.yml
+++ b/modules/nf-core/flye/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md"
       tool_dev_url: "https://github.com/fenderglass/Flye"
       doi: "10.1038/s41592-020-00971-x"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/foldseek/createdb/meta.yml b/modules/nf-core/foldseek/createdb/meta.yml
index 52c101aec4c..27d0a43f057 100644
--- a/modules/nf-core/foldseek/createdb/meta.yml
+++ b/modules/nf-core/foldseek/createdb/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/steineggerlab/foldseek"
       tool_dev_url: "https://github.com/steineggerlab/foldseek"
       doi: "10.1038/s41587-023-01773-0"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/foldseek/easysearch/meta.yml b/modules/nf-core/foldseek/easysearch/meta.yml
index afbbad6c92d..d18cc01dbed 100644
--- a/modules/nf-core/foldseek/easysearch/meta.yml
+++ b/modules/nf-core/foldseek/easysearch/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/steineggerlab/foldseek"
       tool_dev_url: "https://github.com/steineggerlab/foldseek"
       doi: "10.1038/s41587-023-01773-0"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fq/generate/meta.yml b/modules/nf-core/fq/generate/meta.yml
index 644d51a74e3..d31649d052e 100644
--- a/modules/nf-core/fq/generate/meta.yml
+++ b/modules/nf-core/fq/generate/meta.yml
@@ -4,13 +4,14 @@ description: |
 keywords:
   - generate
   - fastq
+  - simulate
 tools:
   - "fq":
       description: "fq is a library to generate and validate FASTQ file pairs."
       homepage: "https://github.com/stjude-rust-labs/fq"
       documentation: "https://github.com/stjude-rust-labs/fq"
       tool_dev_url: "https://github.com/stjude-rust-labs/fq"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fq/lint/meta.yml b/modules/nf-core/fq/lint/meta.yml
index aaa7caab283..f705a26b26e 100644
--- a/modules/nf-core/fq/lint/meta.yml
+++ b/modules/nf-core/fq/lint/meta.yml
@@ -3,13 +3,15 @@ description: fq lint is a FASTQ file pair validator.
 keywords:
   - lint
   - fastq
+  - fq
+  - validate
 tools:
   - "fq":
       description: "fq is a library to generate and validate FASTQ file pairs."
       homepage: "https://github.com/stjude-rust-labs/fq"
       documentation: "https://github.com/stjude-rust-labs/fq"
       tool_dev_url: "https://github.com/stjude-rust-labs/fq"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml
index 6c5e87f3e85..926c5cea03e 100644
--- a/modules/nf-core/fq/subsample/meta.yml
+++ b/modules/nf-core/fq/subsample/meta.yml
@@ -2,6 +2,7 @@ name: "fq_subsample"
 description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args.
 keywords:
   - fastq
+  - sample
   - fq
   - subsample
 tools:
diff --git a/modules/nf-core/galah/meta.yml b/modules/nf-core/galah/meta.yml
index 95b1cd8d31e..1a14d8a9f2b 100644
--- a/modules/nf-core/galah/meta.yml
+++ b/modules/nf-core/galah/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/wwood/galah"
       tool_dev_url: "https://github.com/wwood/galah"
       doi: "10.1111/NODOI"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gamma/gamma/meta.yml b/modules/nf-core/gamma/gamma/meta.yml
index 323e1d7c8ba..24c5c6bcf39 100644
--- a/modules/nf-core/gamma/gamma/meta.yml
+++ b/modules/nf-core/gamma/gamma/meta.yml
@@ -3,6 +3,8 @@ description: Gene Allele Mutation Microbial Assessment
 keywords:
   - gamma
   - gene-calling
+  - microbial
+  - mutation
 tools:
   - "gamma":
       description: "Tool for Gene Allele Mutation Microbial Assessment"
@@ -10,7 +12,7 @@ tools:
       documentation: "https://github.com/rastanton/GAMMA"
       tool_dev_url: "https://github.com/rastanton/GAMMA"
       doi: "10.1093/bioinformatics/btab607"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gangstr/meta.yml b/modules/nf-core/gangstr/meta.yml
index efb5012ec4f..96339533729 100644
--- a/modules/nf-core/gangstr/meta.yml
+++ b/modules/nf-core/gangstr/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/gymreklab/GangSTR"
       tool_dev_url: "https://github.com/gymreklab/GangSTR"
       doi: "10.1093/nar/gkz501"
-      licence: "['GPL v3-or-later']"
+      licence: ["GPL v3-or-later"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gappa/examineassign/meta.yml b/modules/nf-core/gappa/examineassign/meta.yml
index 1753b181150..e70489e6265 100644
--- a/modules/nf-core/gappa/examineassign/meta.yml
+++ b/modules/nf-core/gappa/examineassign/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/lczech/gappa/wiki"
       tool_dev_url: "https://github.com/lczech/gappa"
       doi: "10.1093/bioinformatics/btaa070"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gappa/examinegraft/meta.yml b/modules/nf-core/gappa/examinegraft/meta.yml
index 9dcb56bccb5..76536d0a521 100644
--- a/modules/nf-core/gappa/examinegraft/meta.yml
+++ b/modules/nf-core/gappa/examinegraft/meta.yml
@@ -2,6 +2,9 @@ name: "gappa_examinegraft"
 description: grafts query sequences from phylogenetic placement on the reference tree
 keywords:
   - sort
+  - graft
+  - phylogenetic placement
+  - gappa
 tools:
   - "gappa":
       description: "Genesis Applications for Phylogenetic Placement Analysis"
@@ -9,7 +12,7 @@ tools:
       documentation: "https://github.com/lczech/gappa/wiki"
       tool_dev_url: "https://github.com/lczech/gappa"
       doi: "10.1093/bioinformatics/btaa070"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gappa/examineheattree/meta.yml b/modules/nf-core/gappa/examineheattree/meta.yml
index 35e0c1e4fce..4e59d029e78 100644
--- a/modules/nf-core/gappa/examineheattree/meta.yml
+++ b/modules/nf-core/gappa/examineheattree/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/lczech/gappa/wiki"
       tool_dev_url: "https://github.com/lczech/gappa"
       doi: "10.1093/bioinformatics/btaa070"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml
index 15d9aec41c7..31806e175f0 100644
--- a/modules/nf-core/gatk/indelrealigner/meta.yml
+++ b/modules/nf-core/gatk/indelrealigner/meta.yml
@@ -11,7 +11,12 @@ tools:
       description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
       homepage: "https://gatk.broadinstitute.org/hc/en-us"
       documentation: "https://github.com/broadinstitute/gatk-docs"
-      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
+      licence:
+        [
+          "https://software.broadinstitute.org/gatk/download/licensing",
+          "BSD",
+          "https://www.broadinstitute.org/gatk/about/#licensing",
+        ]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml
index f7cf3c60f22..038b0007274 100644
--- a/modules/nf-core/gatk/realignertargetcreator/meta.yml
+++ b/modules/nf-core/gatk/realignertargetcreator/meta.yml
@@ -12,7 +12,12 @@ tools:
       description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
       homepage: "https://gatk.broadinstitute.org/hc/en-us"
       documentation: "https://github.com/broadinstitute/gatk-docs"
-      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
+      licence:
+        [
+          "https://software.broadinstitute.org/gatk/download/licensing",
+          "BSD",
+          "https://www.broadinstitute.org/gatk/about/#licensing",
+        ]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gatk/unifiedgenotyper/meta.yml b/modules/nf-core/gatk/unifiedgenotyper/meta.yml
index 708815eecd0..652ce63f148 100644
--- a/modules/nf-core/gatk/unifiedgenotyper/meta.yml
+++ b/modules/nf-core/gatk/unifiedgenotyper/meta.yml
@@ -9,7 +9,12 @@ tools:
       description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
       homepage: "https://gatk.broadinstitute.org/hc/en-us"
       documentation: "https://github.com/broadinstitute/gatk-docs"
-      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
+      licence:
+        [
+          "https://software.broadinstitute.org/gatk/download/licensing",
+          "BSD",
+          "https://www.broadinstitute.org/gatk/about/#licensing",
+        ]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml
index 3c6478603e4..264a58922d0 100644
--- a/modules/nf-core/gatk4/collectsvevidence/meta.yml
+++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://gatk.broadinstitute.org/hc/en-us"
       tool_dev_url: "https://github.com/broadinstitute/gatk"
       doi: "10.1158/1538-7445.AM2017-3590"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gatk4/condensedepthevidence/meta.yml b/modules/nf-core/gatk4/condensedepthevidence/meta.yml
index 9ad221f3b01..dffb414bf46 100644
--- a/modules/nf-core/gatk4/condensedepthevidence/meta.yml
+++ b/modules/nf-core/gatk4/condensedepthevidence/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://gatk.broadinstitute.org/hc/en-us"
       tool_dev_url: "https://github.com/broadinstitute/gatk"
       doi: "10.1158/1538-7445.AM2017-3590"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml
index 1bc978e1f1d..2b6033b0b5e 100644
--- a/modules/nf-core/gawk/meta.yml
+++ b/modules/nf-core/gawk/meta.yml
@@ -15,7 +15,7 @@ tools:
       homepage: "https://www.gnu.org/software/gawk/"
       documentation: "https://www.gnu.org/software/gawk/manual/"
       tool_dev_url: "https://www.gnu.org/prep/ftp.html"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gecco/run/meta.yml b/modules/nf-core/gecco/run/meta.yml
index 7bb274d1c67..a2f4a7266bb 100644
--- a/modules/nf-core/gecco/run/meta.yml
+++ b/modules/nf-core/gecco/run/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://gecco.embl.de"
       tool_dev_url: "https://github.com/zellerlab/GECCO"
       doi: "10.1101/2021.05.03.442509"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gem2/gem2bedmappability/meta.yml b/modules/nf-core/gem2/gem2bedmappability/meta.yml
index 8785ff0fd21..a625c9e87ad 100644
--- a/modules/nf-core/gem2/gem2bedmappability/meta.yml
+++ b/modules/nf-core/gem2/gem2bedmappability/meta.yml
@@ -12,7 +12,7 @@ tools:
       description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability."
       homepage: "https://paoloribeca.science/gem"
       # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise)
-      licence: "['Custom']"
+      licence: ["Custom"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gem2/gemindexer/meta.yml b/modules/nf-core/gem2/gemindexer/meta.yml
index 2e43c6e8d54..00152b05649 100644
--- a/modules/nf-core/gem2/gemindexer/meta.yml
+++ b/modules/nf-core/gem2/gemindexer/meta.yml
@@ -11,7 +11,7 @@ tools:
   - "gem2":
       description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability."
       homepage: "https://paoloribeca.science/gem"
-      licence: "['Custom']"
+      licence: ["Custom"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gem2/gemmappability/meta.yml b/modules/nf-core/gem2/gemmappability/meta.yml
index 07d9f14d56a..8157a85a609 100644
--- a/modules/nf-core/gem2/gemmappability/meta.yml
+++ b/modules/nf-core/gem2/gemmappability/meta.yml
@@ -11,7 +11,7 @@ tools:
   - "gem2":
       description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability."
       homepage: "https://paoloribeca.science/gem"
-      licence: "['Custom']"
+      licence: ["Custom"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gem3/gem3indexer/meta.yml b/modules/nf-core/gem3/gem3indexer/meta.yml
index 9618c232023..461289b8683 100644
--- a/modules/nf-core/gem3/gem3indexer/meta.yml
+++ b/modules/nf-core/gem3/gem3indexer/meta.yml
@@ -11,7 +11,7 @@ tools:
   - "gem3":
       description: "The GEM indexer (v3)."
       homepage: "https://github.com/miqalvarez/gem3/tree/gem3-indexer"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/genescopefk/meta.yml b/modules/nf-core/genescopefk/meta.yml
index bc9b2cb83be..b54cfbcd976 100644
--- a/modules/nf-core/genescopefk/meta.yml
+++ b/modules/nf-core/genescopefk/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "A derivative of GenomeScope2.0 modified to work with FastK"
       homepage: "https://github.com/thegenemyers/GENESCOPE.FK"
       tool_dev_url: "https://github.com/thegenemyers/GENESCOPE.FK"
-      licence: "https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml
index 3c876ac588e..2d1ac6d91b5 100644
--- a/modules/nf-core/genmod/annotate/meta.yml
+++ b/modules/nf-core/genmod/annotate/meta.yml
@@ -3,6 +3,8 @@ description: for annotating regions, frequencies, cadd scores
 keywords:
   - annotate
   - genmod
+  - vcf
+  - cadd
   - ranking
 tools:
   - "genmod":
diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml
index dd9001e0451..4dc483d9897 100644
--- a/modules/nf-core/genmod/models/meta.yml
+++ b/modules/nf-core/genmod/models/meta.yml
@@ -3,6 +3,8 @@ description: annotate models of inheritance
 keywords:
   - models
   - genmod
+  - vcf
+  - inheritance
   - ranking
 tools:
   - "genmod":
diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml
index 8998b00c9c6..f81b1325f3f 100644
--- a/modules/nf-core/genmod/score/meta.yml
+++ b/modules/nf-core/genmod/score/meta.yml
@@ -4,6 +4,8 @@ keywords:
   - score
   - ranking
   - genmod
+  - vcf
+  - variants
 tools:
   - "genmod":
       description: "Annotate genetic inheritance models in variant files"
diff --git a/modules/nf-core/genomescope2/meta.yml b/modules/nf-core/genomescope2/meta.yml
index 2c1d5158dd7..f94b647ead1 100644
--- a/modules/nf-core/genomescope2/meta.yml
+++ b/modules/nf-core/genomescope2/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md"
       tool_dev_url: "https://github.com/tbenavi1/genomescope2.0"
       doi: "10.1038/s41467-020-14998-3"
-      licence: "['Apache License, Version 2.0 (Apache-2.0)']"
+      licence: ["Apache License, Version 2.0 (Apache-2.0)"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/genotyphi/parse/meta.yml b/modules/nf-core/genotyphi/parse/meta.yml
index d237904ecf4..8648761e0fd 100644
--- a/modules/nf-core/genotyphi/parse/meta.yml
+++ b/modules/nf-core/genotyphi/parse/meta.yml
@@ -3,13 +3,14 @@ description: Genotype Salmonella Typhi from Mykrobe results
 keywords:
   - genotype
   - Salmonella Typhi
+  - Mykrobe
 tools:
   - "genotyphi":
       description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)"
       homepage: "https://github.com/katholt/genotyphi"
       documentation: "https://github.com/katholt/genotyphi"
       tool_dev_url: "https://github.com/katholt/genotyphi"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml
index ca0074c7a53..b8000288415 100644
--- a/modules/nf-core/geoquery/getgeo/meta.yml
+++ b/modules/nf-core/geoquery/getgeo/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html"
       tool_dev_url: "https://github.com/seandavi/GEOquery"
       doi: "10.1093/bioinformatics/btm254"
-      licence: "MIT"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml
index d0e97a8f319..aaaf47caeb8 100644
--- a/modules/nf-core/gfastats/meta.yml
+++ b/modules/nf-core/gfastats/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://github.com/vgl-hub/gfastats/tree/main/instructions"
       tool_dev_url: "https://github.com/vgl-hub/gfastats"
       doi: "10.1093/bioinformatics/btac460"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gfatools/gfa2fa/meta.yml b/modules/nf-core/gfatools/gfa2fa/meta.yml
index aad4522f56b..06861289d51 100644
--- a/modules/nf-core/gfatools/gfa2fa/meta.yml
+++ b/modules/nf-core/gfatools/gfa2fa/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://github.com/lh3/gfatools"
       tool_dev_url: "https://github.com/lh3/gfatools"
       doi: "no DOI available"
-      licence: "['Unknown']"
+      licence: ["None"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gfatools/stat/meta.yml b/modules/nf-core/gfatools/stat/meta.yml
index 34ea2150ede..725f4fbce44 100644
--- a/modules/nf-core/gfatools/stat/meta.yml
+++ b/modules/nf-core/gfatools/stat/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://github.com/lh3/gfatools"
       tool_dev_url: "https://github.com/lh3/gfatools"
       doi: "no DOI available"
-      licence: "['Unknown']"
+      licence: ["None"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gget/gget/meta.yml b/modules/nf-core/gget/gget/meta.yml
index 08aa182939b..103fd70653f 100644
--- a/modules/nf-core/gget/gget/meta.yml
+++ b/modules/nf-core/gget/gget/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://pachterlab.github.io/gget/"
       tool_dev_url: "https://github.com/pachterlab/gget"
       doi: "10.1093/bioinformatics/btac836"
-      licence: "['BSD-2-clause']"
+      licence: ["BSD-2-clause"]
 input:
   - meta:
       type: map
@@ -21,7 +21,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test' ]
   - files:
-      type: files
+      type: file
       description: |
         Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle.
 output:
diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
index 65fa6218a4a..e500d9e9715 100644
--- a/modules/nf-core/glimpse/chunk/meta.yml
+++ b/modules/nf-core/glimpse/chunk/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/concordance/meta.yml b/modules/nf-core/glimpse/concordance/meta.yml
index c73948f4914..2b2d7195df8 100644
--- a/modules/nf-core/glimpse/concordance/meta.yml
+++ b/modules/nf-core/glimpse/concordance/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml
index da6066add2b..c3b1485c436 100644
--- a/modules/nf-core/glimpse/ligate/meta.yml
+++ b/modules/nf-core/glimpse/ligate/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml
index 696616d37b1..862033b7f83 100644
--- a/modules/nf-core/glimpse/phase/meta.yml
+++ b/modules/nf-core/glimpse/phase/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/sample/meta.yml b/modules/nf-core/glimpse/sample/meta.yml
index 08e27b60c95..36937ec0c26 100644
--- a/modules/nf-core/glimpse/sample/meta.yml
+++ b/modules/nf-core/glimpse/sample/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -22,12 +22,6 @@ input:
       type: file
       description: VCF/BCF file generated using GLIMPSE ligate
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-  - sample:
-      type: parameter
-      description: Samples a likely haplotype pair for each sample, use it in combination with --seed. Option not recommended for general usage, use --solve instead
-  - solve:
-      type: parameter
-      description: Get the most likely haplotype pair for each sample (the random number generator is not used)
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/chunk/meta.yml b/modules/nf-core/glimpse2/chunk/meta.yml
index 1be47538cfd..68c552e43a6 100644
--- a/modules/nf-core/glimpse2/chunk/meta.yml
+++ b/modules/nf-core/glimpse2/chunk/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 requirements:
   - AVX2
 input:
diff --git a/modules/nf-core/glimpse2/concordance/meta.yml b/modules/nf-core/glimpse2/concordance/meta.yml
index 7c82c350480..7d145d2b4b1 100644
--- a/modules/nf-core/glimpse2/concordance/meta.yml
+++ b/modules/nf-core/glimpse2/concordance/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/ligate/meta.yml b/modules/nf-core/glimpse2/ligate/meta.yml
index ffedb344896..7c07973f75b 100644
--- a/modules/nf-core/glimpse2/ligate/meta.yml
+++ b/modules/nf-core/glimpse2/ligate/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/phase/meta.yml b/modules/nf-core/glimpse2/phase/meta.yml
index 0c2f543c64d..183f26be1b5 100644
--- a/modules/nf-core/glimpse2/phase/meta.yml
+++ b/modules/nf-core/glimpse2/phase/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/splitreference/meta.yml b/modules/nf-core/glimpse2/splitreference/meta.yml
index d70f3505874..0eb5b052944 100644
--- a/modules/nf-core/glimpse2/splitreference/meta.yml
+++ b/modules/nf-core/glimpse2/splitreference/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 requirements:
   - AVX2
 input:
diff --git a/modules/nf-core/goleft/indexcov/meta.yml b/modules/nf-core/goleft/indexcov/meta.yml
index ca0c1f9c283..dd0cd655fbe 100644
--- a/modules/nf-core/goleft/indexcov/meta.yml
+++ b/modules/nf-core/goleft/indexcov/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/brentp/goleft"
       tool_dev_url: "https://github.com/brentp/goleft"
       doi: "10.1093/gigascience/gix090"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/goleft/indexsplit/meta.yml b/modules/nf-core/goleft/indexsplit/meta.yml
index 023a25a4ce3..49ee3b4f4eb 100644
--- a/modules/nf-core/goleft/indexsplit/meta.yml
+++ b/modules/nf-core/goleft/indexsplit/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/brentp/goleft"
       tool_dev_url: "https://github.com/brentp/goleft"
       doi: "10.1093/gigascience/gix090"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/graphtyper/genotype/meta.yml b/modules/nf-core/graphtyper/genotype/meta.yml
index 927b0c2869f..b440dce4928 100644
--- a/modules/nf-core/graphtyper/genotype/meta.yml
+++ b/modules/nf-core/graphtyper/genotype/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide"
       tool_dev_url: "https://github.com/DecodeGenetics/graphtyper"
       doi: "10.1038/ng.3964"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml
index 92ec7981fdd..a34a83e83fc 100644
--- a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml
+++ b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide"
       tool_dev_url: "https://github.com/DecodeGenetics/graphtyper"
       doi: "10.1038/ng.3964"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gridss/gridss/meta.yml b/modules/nf-core/gridss/gridss/meta.yml
index bf5539c104f..0f6323605c2 100644
--- a/modules/nf-core/gridss/gridss/meta.yml
+++ b/modules/nf-core/gridss/gridss/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
       tool_dev_url: "https://github.com/PapenfussLab/gridss"
       doi: "10.1186/s13059-021-02423-x"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -20,7 +20,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - inputs:
-      type: file(s)
+      type: file
       description: One or more input BAM/CRAM file(s)
       pattern: "*.{bam,cram}"
   - assembly:
diff --git a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml
index c6b3e1b5939..852e5ea402b 100644
--- a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml
+++ b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
       tool_dev_url: "https://github.com/PapenfussLab/gridss"
       doi: "10.1186/s13059-021-02423-x"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 
 input:
   - meta:
diff --git a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml
index 2b7fc37b0c0..3aea9b8cdd1 100644
--- a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml
+++ b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation"
       tool_dev_url: "https://github.com/PapenfussLab/gridss"
       doi: "10.1186/s13059-021-02423-x"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 
 input:
   - meta:
diff --git a/modules/nf-core/gstama/collapse/meta.yml b/modules/nf-core/gstama/collapse/meta.yml
index 209ba75cd6b..9a25a941a0d 100644
--- a/modules/nf-core/gstama/collapse/meta.yml
+++ b/modules/nf-core/gstama/collapse/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://github.com/GenomeRIK/tama/wiki
       tool_dev_url: https://github.com/sguizard/gs-tama
       doi: 10.1186/s12864-020-07123-7
-      licence: GNU GPL3
+      licence: ["GNU GPL3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml
index 30f6bd7f432..191660b82ae 100644
--- a/modules/nf-core/gubbins/meta.yml
+++ b/modules/nf-core/gubbins/meta.yml
@@ -4,6 +4,7 @@ licence: ["GPL-2.0-only"]
 keywords:
   - recombination
   - alignment
+  - phylogeny
 tools:
   - gubbins:
       description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
diff --git a/modules/nf-core/gvcftools/extractvariants/meta.yml b/modules/nf-core/gvcftools/extractvariants/meta.yml
index 25ae850a9bc..da2b7d884dd 100644
--- a/modules/nf-core/gvcftools/extractvariants/meta.yml
+++ b/modules/nf-core/gvcftools/extractvariants/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://sites.google.com/site/gvcftools/home"
       documentation: "https://sites.google.com/site/gvcftools/home/configuration-and-analysis"
       tool_dev_url: "https://github.com/sequencing/gvcftools"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hapibd/meta.yml b/modules/nf-core/hapibd/meta.yml
index 686ae88bf22..8def0c8d662 100644
--- a/modules/nf-core/hapibd/meta.yml
+++ b/modules/nf-core/hapibd/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md"
       documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md"
       doi: "10.1016/j.ajhg.2020.02.010"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml
index 273b5b1c1ed..abf636f00f9 100644
--- a/modules/nf-core/haplocheck/meta.yml
+++ b/modules/nf-core/haplocheck/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://github.com/genepi/haplocheck"
       tool_dev_url: "https://github.com/genepi/haplocheck"
       doi: 10.1101/gr.256545.119
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/haplogrep2/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml
index 8174218eb48..518c0f97a5c 100644
--- a/modules/nf-core/haplogrep2/classify/meta.yml
+++ b/modules/nf-core/haplogrep2/classify/meta.yml
@@ -1,14 +1,16 @@
 name: "haplogrep2_classify"
 description: classification into haplogroups
 keywords:
-  - haplogroups.
+  - haplogroups
+  - classification
+  - mtDNA
 tools:
   - "haplogrep2":
       description: "A tool for mtDNA haplogroup classification."
       homepage: "https://github.com/seppinho/haplogrep-cmd"
       documentation: "https://github.com/seppinho/haplogrep-cmd"
       tool_dev_url: "https://github.com/seppinho/haplogrep-cmd"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/happy/happy/meta.yml b/modules/nf-core/happy/happy/meta.yml
index 85912cb5012..39ebc64a07e 100644
--- a/modules/nf-core/happy/happy/meta.yml
+++ b/modules/nf-core/happy/happy/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
       documentation: "https://github.com/Illumina/hap.py"
       tool_dev_url: "https://github.com/Illumina/hap.py"
-      licence: "['BSD-2-clause']"
+      licence: ["BSD-2-clause"]
 input:
   - meta:
       type: map
@@ -51,7 +51,7 @@ input:
       description: Stratification file list in TSV format
       pattern: "*.tsv"
   - stratification_beds:
-      type: file(s)
+      type: file
       description: One or more BED files used for stratification (these should be referenced in the stratification TSV)
       pattern: "*.bed"
 output:
diff --git a/modules/nf-core/happy/prepy/meta.yml b/modules/nf-core/happy/prepy/meta.yml
index 646de56df33..e25da5c95b2 100644
--- a/modules/nf-core/happy/prepy/meta.yml
+++ b/modules/nf-core/happy/prepy/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html"
       documentation: "https://github.com/Illumina/hap.py"
       tool_dev_url: "https://github.com/Illumina/hap.py"
-      licence: "['BSD-2-clause']"
+      licence: ["BSD-2-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml
index 3dd2b911be8..30bd60a89ee 100644
--- a/modules/nf-core/happy/sompy/meta.yml
+++ b/modules/nf-core/happy/sompy/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md"
       tool_dev_url: "https://github.com/Illumina/hap.py"
 
-      licence: "['BSD-2-clause']"
+      licence: ["BSD-2-clause"]
 
 input:
   - meta:
diff --git a/modules/nf-core/hicexplorer/hicpca/meta.yml b/modules/nf-core/hicexplorer/hicpca/meta.yml
index 380f882729a..742b6514851 100644
--- a/modules/nf-core/hicexplorer/hicpca/meta.yml
+++ b/modules/nf-core/hicexplorer/hicpca/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://hicexplorer.readthedocs.io"
       tool_dev_url: "https://github.com/deeptools/HiCExplorer"
       doi: "10.1038/s41467-017-02525-w"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml
index c08e8177827..a2a2fbf9dad 100644
--- a/modules/nf-core/hlala/preparegraph/meta.yml
+++ b/modules/nf-core/hlala/preparegraph/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala"
       tool_dev_url: "https://github.com/DiltheyLab/HLA-LA"
       doi: "10.1093/bioinformatics/btz235"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - graph:
       type: directory
diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml
index ede373be504..20c0844aa1d 100644
--- a/modules/nf-core/hlala/typing/meta.yml
+++ b/modules/nf-core/hlala/typing/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala"
       tool_dev_url: "https://github.com/DiltheyLab/HLA-LA"
       doi: "10.1093/bioinformatics/btz235"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hmmer/eslreformat/meta.yml b/modules/nf-core/hmmer/eslreformat/meta.yml
index 7e530d59af4..5fbceea0009 100644
--- a/modules/nf-core/hmmer/eslreformat/meta.yml
+++ b/modules/nf-core/hmmer/eslreformat/meta.yml
@@ -2,6 +2,8 @@ name: "hmmer_eslreformat"
 description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values.
 keywords:
   - sort
+  - hmmer
+  - esl-reformat
 tools:
   - "hmmer":
       description: "Biosequence analysis using profile hidden Markov models"
diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml
index c1ac8f40821..ad266f16b9e 100644
--- a/modules/nf-core/hmmer/hmmalign/meta.yml
+++ b/modules/nf-core/hmmer/hmmalign/meta.yml
@@ -2,6 +2,8 @@ name: hmmer_hmmalign
 description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile
 keywords:
   - alignment
+  - hmm
+  - hmmer
 tools:
   - hmmer:
       description: Biosequence analysis using profile hidden Markov models
diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml
index 4bf6b1cfee9..fb9d5083001 100644
--- a/modules/nf-core/hmmer/hmmbuild/meta.yml
+++ b/modules/nf-core/hmmer/hmmbuild/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "http://hmmer.org/documentation.html"
       tool_dev_url: "https://github.com/EddyRivasLab/hmmer"
       doi: "10.1371/journal.pcbi.1002195"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hmmer/hmmsearch/meta.yml b/modules/nf-core/hmmer/hmmsearch/meta.yml
index a0c39761b39..90a002fdebc 100644
--- a/modules/nf-core/hmmer/hmmsearch/meta.yml
+++ b/modules/nf-core/hmmer/hmmsearch/meta.yml
@@ -28,13 +28,13 @@ input:
       description: Database of sequences in FASTA format
       pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}"
   - write_align:
-      type: val
+      type: string
       description: Flag to write optional alignment output. Specify with 'true' to output
   - write_target:
-      type: val
+      type: string
       description: Flag to write optional per target summary . Specify with 'true' to output
   - write_domain:
-      type: val
+      type: string
       description: Flag to write optional per domain summary. Specify with 'true' to output
 output:
   - meta:
diff --git a/modules/nf-core/htseq/count/meta.yml b/modules/nf-core/htseq/count/meta.yml
index 1a036ffa3c0..9373e680e02 100644
--- a/modules/nf-core/htseq/count/meta.yml
+++ b/modules/nf-core/htseq/count/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://htseq.readthedocs.io/en/latest/"
       documentation: "https://htseq.readthedocs.io/en/latest/index.html"
       doi: "10.1093/bioinformatics/btu638"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml
index 36a7e714f75..002b418f5c8 100644
--- a/modules/nf-core/hypo/meta.yml
+++ b/modules/nf-core/hypo/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/kensung-lab/hypo/blob/master/README.md"
       tool_dev_url: "https://github.com/kensung-lab/hypo"
       doi: "10.1101/2019.12.19.882506"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/idr/meta.yml b/modules/nf-core/idr/meta.yml
index fb7c6944a4c..dc10a3ad0da 100644
--- a/modules/nf-core/idr/meta.yml
+++ b/modules/nf-core/idr/meta.yml
@@ -17,15 +17,15 @@ tools:
       licence: ["GPL v2"]
 input:
   - peaks:
-      type: tuple of two files
+      type: file
       description: BED, narrowPeak or broadPeak files of replicates
       pattern: "*"
   - peak_type:
-      type: value
+      type: string
       description: Type of peak file
       pattern: "{narrowPeak,broadPeak,bed}"
   - prefix:
-      type: value
+      type: string
       description: Prefix for output files
 output:
   - versions:
diff --git a/modules/nf-core/igv/js/meta.yml b/modules/nf-core/igv/js/meta.yml
index 2a261b14d65..48fc3cc57f1 100644
--- a/modules/nf-core/igv/js/meta.yml
+++ b/modules/nf-core/igv/js/meta.yml
@@ -17,7 +17,7 @@ tools:
       documentation: https://github.com/igvteam/igv.js/wiki
       tool_dev_url: https://github.com/igvteam/igv.js
       doi: 10.1093/bioinformatics/btac830
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml
index cb2af37b358..066f08506c8 100644
--- a/modules/nf-core/ilastik/multicut/meta.yml
+++ b/modules/nf-core/ilastik/multicut/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://www.ilastik.org/"
       documentation: "https://www.ilastik.org/documentation/"
       tool_dev_url: "https://github.com/ilastik/ilastik"
-      licence: "GPL3"
+      licence: ["GPL3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml
index 6a9e8babcc7..ad100d9b827 100644
--- a/modules/nf-core/ilastik/pixelclassification/meta.yml
+++ b/modules/nf-core/ilastik/pixelclassification/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://www.ilastik.org/"
       documentation: "https://www.ilastik.org/documentation/"
       tool_dev_url: "https://github.com/ilastik/ilastik"
-      licence: "GPL3"
+      licence: ["GPL3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml
index e984bd35270..ae361dc6da7 100644
--- a/modules/nf-core/interproscan/meta.yml
+++ b/modules/nf-core/interproscan/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://interproscan-docs.readthedocs.io"
       tool_dev_url: "https://github.com/ebi-pf-team/interproscan"
       doi: "10.1093/bioinformatics/btu031"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/iphop/download/meta.yml b/modules/nf-core/iphop/download/meta.yml
index d5184930dbc..b3a31992e7b 100644
--- a/modules/nf-core/iphop/download/meta.yml
+++ b/modules/nf-core/iphop/download/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://bitbucket.org/srouxjgi/iphop/src/main/
       tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/
       doi: "10.1371/journal.pbio.3002083"
-      licence: "['Modified GPL v3']"
+      licence: ["Modified GPL v3"]
 output:
   - iphop_db:
       type: directory
diff --git a/modules/nf-core/iphop/predict/meta.yml b/modules/nf-core/iphop/predict/meta.yml
index 003343555b3..ce267dd13be 100644
--- a/modules/nf-core/iphop/predict/meta.yml
+++ b/modules/nf-core/iphop/predict/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://bitbucket.org/srouxjgi/iphop/src/main/
       tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/
       doi: "10.1371/journal.pbio.3002083"
-      licence: "['Modified GPL v3']"
+      licence: ["Modified GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/islandpath/meta.yml b/modules/nf-core/islandpath/meta.yml
index 0f714621f08..98d108e3595 100644
--- a/modules/nf-core/islandpath/meta.yml
+++ b/modules/nf-core/islandpath/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: https://github.com/brinkmanlab/islandpath#readme
       tool_dev_url: https://github.com/brinkmanlab/islandpath
       doi: "10.1093/bioinformatics/bty095"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ismapper/meta.yml b/modules/nf-core/ismapper/meta.yml
index 3d1f09cdc56..12d020002b1 100644
--- a/modules/nf-core/ismapper/meta.yml
+++ b/modules/nf-core/ismapper/meta.yml
@@ -3,6 +3,7 @@ description: Identify insertion sites positions in bacterial genomes
 keywords:
   - fastq
   - insertion sequences
+  - bacterial genomes
 tools:
   - ismapper:
       description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.
diff --git a/modules/nf-core/isoseq3/cluster/meta.yml b/modules/nf-core/isoseq3/cluster/meta.yml
index 6089116fb3a..c830eea624d 100644
--- a/modules/nf-core/isoseq3/cluster/meta.yml
+++ b/modules/nf-core/isoseq3/cluster/meta.yml
@@ -2,6 +2,9 @@ name: isoseq3_cluster
 description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
 keywords:
   - cluster
+  - isoseq3
+  - pacbio
+  - consensus
 tools:
   - isoseq3:
       description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
diff --git a/modules/nf-core/jasminesv/meta.yml b/modules/nf-core/jasminesv/meta.yml
index e53ed304bde..7327ded1e4a 100644
--- a/modules/nf-core/jasminesv/meta.yml
+++ b/modules/nf-core/jasminesv/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual"
       documentation: "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual"
       tool_dev_url: "https://github.com/mkirsche/Jasmine"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -20,12 +20,12 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcfs:
-      type: files
+      type: file
       description: |
         The VCF files that need to be merged
       pattern: "*.{vcf,vcf.gz}"
   - bams:
-      type: files
+      type: file
       description: Optional - The BAM files from which the VCFs were created
       pattern: "*.bam"
   - sample_dists:
diff --git a/modules/nf-core/jupyternotebook/meta.yml b/modules/nf-core/jupyternotebook/meta.yml
index 216645d3db4..c036f60624d 100644
--- a/modules/nf-core/jupyternotebook/meta.yml
+++ b/modules/nf-core/jupyternotebook/meta.yml
@@ -15,19 +15,19 @@ tools:
       homepage: https://github.com/mwouts/jupytext/
       documentation: https://jupyter.org/documentation
       tool_dev_url: https://github.com/mwouts/jupytext/
-      licence: "MIT"
+      licence: ["MIT"]
   - papermill:
       description: Parameterize, execute, and analyze notebooks
       homepage: https://github.com/nteract/papermill
       documentation: http://papermill.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/nteract/papermill
-      licence: "BSD 3-clause"
+      licence: ["BSD 3-clause"]
   - nbconvert:
       description: Parameterize, execute, and analyze notebooks
       homepage: https://nbconvert.readthedocs.io/en/latest/
       documentation: https://nbconvert.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/jupyter/nbconvert
-      licence: "BSD 3-clause"
+      licence: ["BSD 3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kaiju/kaiju2table/meta.yml b/modules/nf-core/kaiju/kaiju2table/meta.yml
index 0f62374e8c5..28568aed027 100644
--- a/modules/nf-core/kaiju/kaiju2table/meta.yml
+++ b/modules/nf-core/kaiju/kaiju2table/meta.yml
@@ -1,8 +1,10 @@
 name: "kaiju_kaiju2table"
-description: write your description here
+description: Converts Kaiju's output file(s) into a summary table for a given taxonomic rank, e.g., genus.
 keywords:
   - classify
   - metagenomics
+  - kaiju
+  - taxonomic rank
   - taxonomic profiling
 tools:
   - kaiju:
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index 7491248c8aa..5612bb30923 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://www.kallistobus.tools/
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
-      licence: MIT License
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml
index 00be51431d8..8538cba3e08 100644
--- a/modules/nf-core/kallistobustools/ref/meta.yml
+++ b/modules/nf-core/kallistobustools/ref/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: https://kb-python.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/pachterlab/kb_python
       doi: "10.22002/D1.1876"
-      licence: MIT License
+      licence: ["MIT License"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/kat/hist/meta.yml b/modules/nf-core/kat/hist/meta.yml
index 2d6d783d6c9..c933c9582c3 100644
--- a/modules/nf-core/kat/hist/meta.yml
+++ b/modules/nf-core/kat/hist/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: https://kat.readthedocs.io/en/latest/index.html
       tool_dev_url: https://github.com/TGAC/KAT
       doi: 10.1093/bioinformatics/btw663
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kleborate/meta.yml b/modules/nf-core/kleborate/meta.yml
index c5f4673e347..a557b977395 100644
--- a/modules/nf-core/kleborate/meta.yml
+++ b/modules/nf-core/kleborate/meta.yml
@@ -3,6 +3,7 @@ description: Kleborate is a tool to screen genome assemblies of Klebsiella pneum
 keywords:
   - screening assemblies
   - Klebsiella pneumoniae
+  - KpSC
 tools:
   - kleborate:
       description: Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest
@@ -18,7 +19,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - fastas:
-      type: files
+      type: file
       description: Klebsiella genome assemblies to be screened
       pattern: "*.fasta"
 output:
diff --git a/modules/nf-core/kmcp/compute/meta.yml b/modules/nf-core/kmcp/compute/meta.yml
index 12b9c9d0ae0..20cfe4a2c04 100644
--- a/modules/nf-core/kmcp/compute/meta.yml
+++ b/modules/nf-core/kmcp/compute/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/shenwei356/kmcp#documents"
       tool_dev_url: "https://github.com/shenwei356/kmcp"
       doi: "10.1093/bioinformatics/btac845"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kmcp/index/meta.yml b/modules/nf-core/kmcp/index/meta.yml
index de5f9718f3a..841f5a3cdff 100644
--- a/modules/nf-core/kmcp/index/meta.yml
+++ b/modules/nf-core/kmcp/index/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://github.com/shenwei356/kmcp#documents"
       tool_dev_url: "https://github.com/shenwei356/kmcp"
       doi: "10.1093/bioinformatics/btac845"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kmcp/merge/meta.yml b/modules/nf-core/kmcp/merge/meta.yml
index a586a21cb74..cd1134ad994 100644
--- a/modules/nf-core/kmcp/merge/meta.yml
+++ b/modules/nf-core/kmcp/merge/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/shenwei356/kmcp#documents"
       tool_dev_url: "https://github.com/shenwei356/kmcp"
       doi: "10.1093/bioinformatics/btac845"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kmcp/profile/meta.yml b/modules/nf-core/kmcp/profile/meta.yml
index e3ae1f0c6d7..ffd0db4099e 100644
--- a/modules/nf-core/kmcp/profile/meta.yml
+++ b/modules/nf-core/kmcp/profile/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://bioinf.shenwei.me/kmcp/usage/#profile"
       tool_dev_url: "https://github.com/shenwei356/kmcp"
       doi: "10.1093/bioinformatics/btac845"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kmcp/search/meta.yml b/modules/nf-core/kmcp/search/meta.yml
index 3bec8317c61..0d774742020 100644
--- a/modules/nf-core/kmcp/search/meta.yml
+++ b/modules/nf-core/kmcp/search/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/shenwei356/kmcp#documents"
       tool_dev_url: "https://github.com/shenwei356/kmcp"
       doi: "10.1093/bioinformatics/btac845"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/kofamscan/meta.yml b/modules/nf-core/kofamscan/meta.yml
index 7876e3ace0e..06f2872a4e8 100644
--- a/modules/nf-core/kofamscan/meta.yml
+++ b/modules/nf-core/kofamscan/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/takaram/kofam_scan"
       tool_dev_url: "https://github.com/takaram/kofam_scan"
       doi: "10.1093/bioinformatics/btz859"
-      licence: "['MIT License']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/krona/ktimporttext/meta.yml b/modules/nf-core/krona/ktimporttext/meta.yml
index 0521a1bdadc..5288ea0b47e 100644
--- a/modules/nf-core/krona/ktimporttext/meta.yml
+++ b/modules/nf-core/krona/ktimporttext/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
       tool_dev_url: https://github.com/marbl/Krona
       doi: 10.1186/1471-2105-12-385
-      licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
+      licence: ["https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml
index 39943833239..e15c1bc20ad 100644
--- a/modules/nf-core/legsta/meta.yml
+++ b/modules/nf-core/legsta/meta.yml
@@ -3,6 +3,7 @@ description: Typing of clinical and environmental isolates of Legionella pneumop
 keywords:
   - bacteria
   - legionella
+  - typing
 tools:
   - legsta:
       description: In silico Legionella pneumophila Sequence Based Typing
diff --git a/modules/nf-core/lofreq/somatic/meta.yml b/modules/nf-core/lofreq/somatic/meta.yml
index e165312dd1e..f78b05a9a94 100644
--- a/modules/nf-core/lofreq/somatic/meta.yml
+++ b/modules/nf-core/lofreq/somatic/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://csb5.github.io/lofreq/
       documentation: https://csb5.github.io/lofreq/commands/
       doi: 10.1093/nar/gks918
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mageck/count/meta.yml b/modules/nf-core/mageck/count/meta.yml
index 3e3ad475b73..9281809dd97 100644
--- a/modules/nf-core/mageck/count/meta.yml
+++ b/modules/nf-core/mageck/count/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://sourceforge.net/p/mageck/wiki/Home/"
       documentation: "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command"
       doi: "10.1186/s13059-014-0554-4"
-      licence: "['BSD License']"
+      licence: ["BSD License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mageck/mle/meta.yml b/modules/nf-core/mageck/mle/meta.yml
index bdb3d0cbc69..b8be3261882 100644
--- a/modules/nf-core/mageck/mle/meta.yml
+++ b/modules/nf-core/mageck/mle/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://sourceforge.net/p/mageck/wiki/Home/"
       tool_dev_url: "https://bitbucket.org/liulab/mageck/src"
       doi: "10.1186/s13059-015-0843-6"
-      licence: "['BSD License']"
+      licence: ["BSD License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mageck/test/meta.yml b/modules/nf-core/mageck/test/meta.yml
index 4749d4d7fe6..2337dfe3103 100644
--- a/modules/nf-core/mageck/test/meta.yml
+++ b/modules/nf-core/mageck/test/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://sourceforge.net/p/mageck/wiki/Home/"
       tool_dev_url: "https://bitbucket.org/liulab/mageck/src"
       doi: "10.1186/s13059-015-0843-6"
-      licence: "['BSD License']"
+      licence: ["BSD License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mapad/index/meta.yml b/modules/nf-core/mapad/index/meta.yml
index 725eeacff22..2c94d9fc6a9 100644
--- a/modules/nf-core/mapad/index/meta.yml
+++ b/modules/nf-core/mapad/index/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/mpieva/mapAD"
       documentation: "https://github.com/mpieva/mapAD"
       tool_dev_url: "https://github.com/mpieva/mapAD"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mapad/map/meta.yml b/modules/nf-core/mapad/map/meta.yml
index 4655662214b..1ca5e9d2cd2 100644
--- a/modules/nf-core/mapad/map/meta.yml
+++ b/modules/nf-core/mapad/map/meta.yml
@@ -32,7 +32,7 @@ tools:
       homepage: "https://github.com/mpieva/mapAD"
       documentation: "https://github.com/mpieva/mapAD"
       tool_dev_url: "https://github.com/mpieva/mapAD"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mash/dist/meta.yml b/modules/nf-core/mash/dist/meta.yml
index 32e200f7bf6..cf69df4ac7e 100644
--- a/modules/nf-core/mash/dist/meta.yml
+++ b/modules/nf-core/mash/dist/meta.yml
@@ -1,7 +1,9 @@
 name: mash_dist
 description: Calculate Mash distances between reference and query seqeunces
 keywords:
-  - mash/dist
+  - mash distance
+  - fasta
+  - mash
 tools:
   - mash:
       description: Fast sequence distance estimator that uses MinHash
diff --git a/modules/nf-core/maxquant/lfq/meta.yml b/modules/nf-core/maxquant/lfq/meta.yml
index 200e103693b..c6a8482c6f5 100644
--- a/modules/nf-core/maxquant/lfq/meta.yml
+++ b/modules/nf-core/maxquant/lfq/meta.yml
@@ -2,6 +2,9 @@ name: maxquant_lfq
 description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
 keywords:
   - sort
+  - maxquant
+  - proteomics
+  - label-free
 tools:
   - maxquant:
       description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
diff --git a/modules/nf-core/mcquant/meta.yml b/modules/nf-core/mcquant/meta.yml
index 44623f925cd..1343a26b1a0 100644
--- a/modules/nf-core/mcquant/meta.yml
+++ b/modules/nf-core/mcquant/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/labsyspharm/quantification/blob/master/README.md"
       tool_dev_url: "https://github.com/labsyspharm/quantification"
       doi: 10.1038/s41592-021-01308-y
-      licence: ""
+      licence: ["None"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mcroni/meta.yml b/modules/nf-core/mcroni/meta.yml
index 895e8fc3cc5..b342152e4b1 100644
--- a/modules/nf-core/mcroni/meta.yml
+++ b/modules/nf-core/mcroni/meta.yml
@@ -3,13 +3,15 @@ description: Analysis of mcr-1 gene (mobilized colistin resistance) for sequence
 keywords:
   - resistance
   - fasta
+  - sequence variation
+  - mcr-1
 tools:
   - "mcroni":
       description: "Scripts for finding and processing promoter variants upstream of mcr-1"
       homepage: "https://github.com/liampshaw/mcroni"
       documentation: "https://github.com/liampshaw/mcroni"
       tool_dev_url: "https://github.com/liampshaw/mcroni"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml
index eb6e5bc90c6..a673d42d572 100644
--- a/modules/nf-core/md5sum/meta.yml
+++ b/modules/nf-core/md5sum/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: Create an MD5 (128-bit) checksum
       homepage: "https://www.gnu.org"
       documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html"
-      licence: GPLv3+
+      licence: ["GPLv3+"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/megan/daa2info/meta.yml b/modules/nf-core/megan/daa2info/meta.yml
index 7530f7da4d1..5b1c7e36638 100644
--- a/modules/nf-core/megan/daa2info/meta.yml
+++ b/modules/nf-core/megan/daa2info/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html"
       tool_dev_url: "https://github.com/husonlab/megan-ce"
       doi: "10.1371/journal.pcbi.1004957"
-      licence: "['GPL >=3']"
+      licence: ["GPL >=3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml
index af3dd96c147..158c86742fa 100644
--- a/modules/nf-core/megan/rma2info/meta.yml
+++ b/modules/nf-core/megan/rma2info/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html"
       tool_dev_url: "https://github.com/husonlab/megan-ce"
       doi: "10.1371/journal.pcbi.1004957"
-      licence: "['GPL >=3']"
+      licence: ["GPL >=3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/merqury/meta.yml b/modules/nf-core/merqury/meta.yml
index 88825386833..bc7d64dafed 100644
--- a/modules/nf-core/merqury/meta.yml
+++ b/modules/nf-core/merqury/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "Evaluate genome assemblies with k-mers and more."
       tool_dev_url: "https://github.com/marbl/merqury"
       doi: "10.1186/s13059-020-02134-9"
-      licence: "['PUBLIC DOMAIN']"
+      licence: ["Public Domain"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/merquryfk/katcomp/meta.yml b/modules/nf-core/merquryfk/katcomp/meta.yml
index ee6650cb48d..05dd4565307 100644
--- a/modules/nf-core/merquryfk/katcomp/meta.yml
+++ b/modules/nf-core/merquryfk/katcomp/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "FastK based version of Merqury"
       homepage: "https://github.com/thegenemyers/MERQURY.FK"
       tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK"
-      licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/merquryfk/katgc/meta.yml b/modules/nf-core/merquryfk/katgc/meta.yml
index f39322b1b31..f15eafc5706 100644
--- a/modules/nf-core/merquryfk/katgc/meta.yml
+++ b/modules/nf-core/merquryfk/katgc/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: "FastK based version of Merqury"
       homepage: "https://github.com/thegenemyers/MERQURY.FK"
       tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK"
-      licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml
index 7d4af796b73..e4527adc6c2 100644
--- a/modules/nf-core/merquryfk/merquryfk/meta.yml
+++ b/modules/nf-core/merquryfk/merquryfk/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "FastK based version of Merqury"
       homepage: "https://github.com/thegenemyers/MERQURY.FK"
       tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK"
-      licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/merquryfk/ploidyplot/meta.yml b/modules/nf-core/merquryfk/ploidyplot/meta.yml
index 2cb0eb19921..62fa9857b18 100644
--- a/modules/nf-core/merquryfk/ploidyplot/meta.yml
+++ b/modules/nf-core/merquryfk/ploidyplot/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "FastK based version of Merqury"
       homepage: "https://github.com/thegenemyers/MERQURY.FK"
       tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK"
-      licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"
+      licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml
index a4de42e0bcc..68eac6d0b14 100644
--- a/modules/nf-core/meryl/count/meta.yml
+++ b/modules/nf-core/meryl/count/meta.yml
@@ -3,13 +3,15 @@ description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
   - k-mer
   - count
+  - meryl
+  - k-mer count
 tools:
   - "meryl":
       description: "A genomic k-mer counter (and sequence utility) with nice features. "
       homepage: "https://github.com/marbl/meryl"
       documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
       tool_dev_url: "https://github.com/marbl/meryl"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/meryl/histogram/meta.yml b/modules/nf-core/meryl/histogram/meta.yml
index f8d2b43f9c0..35c51dbc954 100644
--- a/modules/nf-core/meryl/histogram/meta.yml
+++ b/modules/nf-core/meryl/histogram/meta.yml
@@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
   - k-mer
   - histogram
+  - meryl
 tools:
   - "meryl":
       description: "A genomic k-mer counter (and sequence utility) with nice features. "
       homepage: "https://github.com/marbl/meryl"
       documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
       tool_dev_url: "https://github.com/marbl/meryl"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml
index 9b46f7b9e51..6926e21f106 100644
--- a/modules/nf-core/meryl/unionsum/meta.yml
+++ b/modules/nf-core/meryl/unionsum/meta.yml
@@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
   - k-mer
   - unionsum
+  - meryl
 tools:
   - "meryl":
       description: "A genomic k-mer counter (and sequence utility) with nice features. "
       homepage: "https://github.com/marbl/meryl"
       documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
       tool_dev_url: "https://github.com/marbl/meryl"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/metaeuk/easypredict/meta.yml b/modules/nf-core/metaeuk/easypredict/meta.yml
index 0bea1ccb5de..3943926ca3d 100644
--- a/modules/nf-core/metaeuk/easypredict/meta.yml
+++ b/modules/nf-core/metaeuk/easypredict/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/soedinglab/metaeuk
       tool_dev_url: https://github.com/soedinglab/metaeuk
       doi: "10.1186/s40168-020-00808-x"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/midas/run/meta.yml b/modules/nf-core/midas/run/meta.yml
index fae9fd155b6..e41505ebd1c 100644
--- a/modules/nf-core/midas/run/meta.yml
+++ b/modules/nf-core/midas/run/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/snayfach/MIDAS"
       tool_dev_url: "https://github.com/snayfach/MIDAS"
       doi: "10.1101/gr.201863.115"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml
index 0324102768e..7d0d2badcf6 100644
--- a/modules/nf-core/minia/meta.yml
+++ b/modules/nf-core/minia/meta.yml
@@ -2,6 +2,8 @@ name: minia
 description: Minia is a short-read assembler based on a de Bruijn graph
 keywords:
   - assembly
+  - short-read
+  - de-bruijn
 tools:
   - minia:
       description: |
diff --git a/modules/nf-core/miranda/meta.yml b/modules/nf-core/miranda/meta.yml
index d3950fd1972..2f551da0def 100644
--- a/modules/nf-core/miranda/meta.yml
+++ b/modules/nf-core/miranda/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://cbio.mskcc.org/miRNA2003/miranda.html"
       documentation: "https://cbio.mskcc.org/miRNA2003/miranda.html"
       doi: "10.1186/gb-2003-5-1-r1"
-      licence: "GNU Public License"
+      licence: ["GNU Public License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/mobsuite/recon/meta.yml b/modules/nf-core/mobsuite/recon/meta.yml
index 9f9f381367b..06f11066873 100644
--- a/modules/nf-core/mobsuite/recon/meta.yml
+++ b/modules/nf-core/mobsuite/recon/meta.yml
@@ -3,6 +3,8 @@ description: A tool to reconstruct plasmids in bacterial assemblies
 keywords:
   - bacteria
   - plasmid
+  - assembly
+  - reconstruct
 tools:
   - mobsuite:
       description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
diff --git a/modules/nf-core/motus/downloaddb/meta.yml b/modules/nf-core/motus/downloaddb/meta.yml
index 63df66fe059..6cf509e97ee 100644
--- a/modules/nf-core/motus/downloaddb/meta.yml
+++ b/modules/nf-core/motus/downloaddb/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/motu-tool/mOTUs/wiki"
       tool_dev_url: "https://github.com/motu-tool/mOTUs"
       doi: "10.1186/s40168-022-01410-z"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - motus_downloaddb:
       type: directory
diff --git a/modules/nf-core/motus/merge/meta.yml b/modules/nf-core/motus/merge/meta.yml
index e8dca6f812a..0d7af231a9b 100644
--- a/modules/nf-core/motus/merge/meta.yml
+++ b/modules/nf-core/motus/merge/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://github.com/motu-tool/mOTUs/wiki"
       tool_dev_url: "https://github.com/motu-tool/mOTUs"
       doi: "10.1186/s40168-022-01410-z"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - input:
       type: file
diff --git a/modules/nf-core/msisensor/msi/meta.yml b/modules/nf-core/msisensor/msi/meta.yml
index bec1ee56e6f..b28b98fb0b2 100644
--- a/modules/nf-core/msisensor/msi/meta.yml
+++ b/modules/nf-core/msisensor/msi/meta.yml
@@ -1,7 +1,10 @@
 name: msisensor_msi
 description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
 keywords:
-  - homoploymer,microsatellite
+  - homoploymer
+  - microsatellite
+  - msi
+  - tumor
 tools:
   - msisensor:
       description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
diff --git a/modules/nf-core/msisensor/scan/meta.yml b/modules/nf-core/msisensor/scan/meta.yml
index 26836b9dc85..15594bb9eff 100644
--- a/modules/nf-core/msisensor/scan/meta.yml
+++ b/modules/nf-core/msisensor/scan/meta.yml
@@ -1,7 +1,10 @@
 name: msisensor_scan
 description: Scan a reference genome to get microsatellite & homopolymer information
 keywords:
-  - homoploymer,microsatellite
+  - homoploymer
+  - microsatellite
+  - msi
+  - instability
 tools:
   - msisensor:
       description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
diff --git a/modules/nf-core/msisensor2/msi/meta.yml b/modules/nf-core/msisensor2/msi/meta.yml
index b930de3f47b..4c6297e79a7 100644
--- a/modules/nf-core/msisensor2/msi/meta.yml
+++ b/modules/nf-core/msisensor2/msi/meta.yml
@@ -2,13 +2,16 @@ name: "msisensor2_msi"
 description: msisensor2 detection of MSI regions.
 keywords:
   - msi
+  - microsatellite
+  - microsatellite instability
+  - tumor
 tools:
   - "msisensor2":
       description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data."
       homepage: "https://github.com/niu-lab/msisensor2"
       documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md"
       tool_dev_url: "https://github.com/niu-lab/msisensor2"
-      licence: "GPL-3.0"
+      licence: ["GPL-3.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/msisensor2/scan/meta.yml b/modules/nf-core/msisensor2/scan/meta.yml
index 2d97e91af4b..cc01878737b 100644
--- a/modules/nf-core/msisensor2/scan/meta.yml
+++ b/modules/nf-core/msisensor2/scan/meta.yml
@@ -2,20 +2,22 @@ name: "msisensor2_scan"
 description: msisensor2 detection of MSI regions.
 keywords:
   - msi
+  - microsatellite
+  - instability
 tools:
   - "msisensor2":
       description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data."
       homepage: "https://github.com/niu-lab/msisensor2"
       documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md"
       tool_dev_url: "https://github.com/niu-lab/msisensor2"
-      licence: "GPL-3.0"
+      licence: ["GPL-3.0"]
 input:
   - fasta:
       type: file
       description: Path to reference genome.
       pattern: "*.fasta"
   - output:
-      type: val
+      type: string
       description: Name of output MSI scan to write.
 output:
   - versions:
diff --git a/modules/nf-core/multivcfanalyzer/meta.yml b/modules/nf-core/multivcfanalyzer/meta.yml
index 4c35c11154d..99bfe8dfd9b 100644
--- a/modules/nf-core/multivcfanalyzer/meta.yml
+++ b/modules/nf-core/multivcfanalyzer/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/alexherbig/MultiVCFAnalyzer"
       tool_dev_url: "https://github.com/alexherbig/MultiVCFAnalyzer"
       doi: "10.1038/nature13591"
-      licence: "['GPL >=3']"
+      licence: ["GPL >=3"]
 input:
   - vcfs:
       type: file
@@ -48,10 +48,10 @@ input:
         Minimum number of a reads that a position must be covered by to be
         reported
   - homozygous_freq:
-      type: number
+      type: float
       description: Fraction of reads a base must have to be called 'homozygous'
   - heterozygous_freq:
-      type: mumber
+      type: float
       description: |
         Fraction of which whereby if a call falls above this value, and lower
         than the homozygous threshold, a base will be called 'heterozygous'.
diff --git a/modules/nf-core/muscle/meta.yml b/modules/nf-core/muscle/meta.yml
index 37c898f3f55..c02468ab915 100644
--- a/modules/nf-core/muscle/meta.yml
+++ b/modules/nf-core/muscle/meta.yml
@@ -3,6 +3,7 @@ description: MUSCLE is a program for creating multiple alignments of amino acid
 keywords:
   - msa
   - multiple sequence alignment
+  - alignment
 tools:
   - muscle:
       description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
diff --git a/modules/nf-core/mykrobe/predict/meta.yml b/modules/nf-core/mykrobe/predict/meta.yml
index 4d0862d87c9..ad5652ada18 100644
--- a/modules/nf-core/mykrobe/predict/meta.yml
+++ b/modules/nf-core/mykrobe/predict/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/Mykrobe-tools/mykrobe/wiki"
       tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe"
       doi: "10.1038/ncomms10063"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/nanocomp/meta.yml b/modules/nf-core/nanocomp/meta.yml
index 366c88e1992..85ddf0cd28f 100755
--- a/modules/nf-core/nanocomp/meta.yml
+++ b/modules/nf-core/nanocomp/meta.yml
@@ -11,7 +11,7 @@ tools:
       description: "Compare multiple runs of long read sequencing data and alignments"
       homepage: "https://github.com/wdecoster/nanocomp"
       documentation: "https://github.com/wdecoster/nanocomp"
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/nanolyse/meta.yml b/modules/nf-core/nanolyse/meta.yml
index 375ad9bc1dc..3364cdcdbd2 100644
--- a/modules/nf-core/nanolyse/meta.yml
+++ b/modules/nf-core/nanolyse/meta.yml
@@ -1,7 +1,9 @@
 name: nanolyse
 description: DNA contaminant removal using NanoLyse
 keywords:
-  - contaminant_removal
+  - contaminant removal
+  - DNA
+  - contaminant
 tools:
   - nanolyse:
       description: |
diff --git a/modules/nf-core/nanomonsv/parse/meta.yml b/modules/nf-core/nanomonsv/parse/meta.yml
index 3c8d1098731..db42b42adbd 100644
--- a/modules/nf-core/nanomonsv/parse/meta.yml
+++ b/modules/nf-core/nanomonsv/parse/meta.yml
@@ -20,7 +20,7 @@ tools:
       documentation: https://github.com/friend1ws/nanomonsv#commands
       tool_dev_url: https://github.com/friend1ws/nanomonsv
       doi: "10.1101/2020.07.22.214262 "
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml
index f3fb403e84c..7494b0ed773 100644
--- a/modules/nf-core/nextclade/datasetget/meta.yml
+++ b/modules/nf-core/nextclade/datasetget/meta.yml
@@ -30,7 +30,7 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - prefix:
-      type: path
+      type: directory
       description: A directory containing the dataset files needed for nextclade run
       pattern: "prefix"
 authors:
diff --git a/modules/nf-core/nextclade/run/meta.yml b/modules/nf-core/nextclade/run/meta.yml
index ceebfe20e57..b1fc35755f7 100644
--- a/modules/nf-core/nextclade/run/meta.yml
+++ b/modules/nf-core/nextclade/run/meta.yml
@@ -18,7 +18,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - dataset:
-      type: path
+      type: directory
       description: Path containing the dataset files obtained by running nextclade dataset get
       pattern: "*"
   - fasta:
diff --git a/modules/nf-core/ngmerge/meta.yml b/modules/nf-core/ngmerge/meta.yml
index 4e07ea1a623..7e83a14a0af 100644
--- a/modules/nf-core/ngmerge/meta.yml
+++ b/modules/nf-core/ngmerge/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/jsh58/NGmerge"
       tool_dev_url: "https://github.com/jsh58/NGmerge"
       doi: "10.1186/s12859-018-2579-2"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml
index 997bc06e7d4..a0f9fa774b4 100644
--- a/modules/nf-core/ngsbits/samplegender/meta.yml
+++ b/modules/nf-core/ngsbits/samplegender/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/imgag/ngs-bits"
       documentation: "https://github.com/imgag/ngs-bits"
       tool_dev_url: "https://github.com/imgag/ngs-bits"
-      licence: "['MIT license']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/nucmer/meta.yml b/modules/nf-core/nucmer/meta.yml
index 52d876ae6ba..9ec0d76add2 100644
--- a/modules/nf-core/nucmer/meta.yml
+++ b/modules/nf-core/nucmer/meta.yml
@@ -1,8 +1,9 @@
 name: nucmer
 description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
 keywords:
-  - align
+  - alignment
   - nucleotide
+  - multiple sequence alignment
 tools:
   - nucmer:
       description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
diff --git a/modules/nf-core/oncocnv/meta.yml b/modules/nf-core/oncocnv/meta.yml
index 48d3e11b500..10df50329de 100644
--- a/modules/nf-core/oncocnv/meta.yml
+++ b/modules/nf-core/oncocnv/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/BoevaLab/ONCOCNV/blob/master/README.md"
       tool_dev_url: "https://github.com/BoevaLab/ONCOCNV/"
       doi: "10.1093/bioinformatics/btu436"
-      licence: "GPL-3.0-or-later"
+      licence: ["GPL-3.0-or-later"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/openms/idfilter/meta.yml b/modules/nf-core/openms/idfilter/meta.yml
index 2b1607466c7..2fcbfcf6385 100644
--- a/modules/nf-core/openms/idfilter/meta.yml
+++ b/modules/nf-core/openms/idfilter/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://openms.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/OpenMS/OpenMS"
       doi: "10.1038/nmeth.3959"
-      licence: "['BSD']"
+      licence: ["BSD"]
 
 input:
   - meta:
diff --git a/modules/nf-core/openms/idmerger/meta.yml b/modules/nf-core/openms/idmerger/meta.yml
index 32fa27bf28f..efa79491b9f 100644
--- a/modules/nf-core/openms/idmerger/meta.yml
+++ b/modules/nf-core/openms/idmerger/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://openms.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/OpenMS/OpenMS"
       doi: "10.1038/nmeth.3959"
-      licence: "['BSD']"
+      licence: ["BSD"]
 
 input:
   - meta:
diff --git a/modules/nf-core/openms/peakpickerhires/meta.yml b/modules/nf-core/openms/peakpickerhires/meta.yml
index 28765e09f00..0ff2f13afa2 100644
--- a/modules/nf-core/openms/peakpickerhires/meta.yml
+++ b/modules/nf-core/openms/peakpickerhires/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://openms.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/OpenMS/OpenMS"
       doi: "10.1038/nmeth.3959"
-      licence: "['BSD']"
+      licence: ["BSD"]
 
 input:
   - meta:
diff --git a/modules/nf-core/pairtools/dedup/meta.yml b/modules/nf-core/pairtools/dedup/meta.yml
index 54f06ea1a83..7fed17437e0 100644
--- a/modules/nf-core/pairtools/dedup/meta.yml
+++ b/modules/nf-core/pairtools/dedup/meta.yml
@@ -2,6 +2,9 @@ name: pairtools_dedup
 description: Find and remove PCR/optical duplicates
 keywords:
   - dedup
+  - pairtools
+  - PCR
+  - duplicates
 tools:
   - pairtools:
       description: CLI tools to process mapped Hi-C data
diff --git a/modules/nf-core/pairtools/flip/meta.yml b/modules/nf-core/pairtools/flip/meta.yml
index ed7fc0f0c7a..b1e98bedd94 100644
--- a/modules/nf-core/pairtools/flip/meta.yml
+++ b/modules/nf-core/pairtools/flip/meta.yml
@@ -2,6 +2,10 @@ name: pairtools_flip
 description: Flip pairs to get an upper-triangular matrix
 keywords:
   - flip
+  - pairtools
+  - Hi-C
+  - HiC
+  - triangular matrix
 tools:
   - pairtools:
       description: CLI tools to process mapped Hi-C data
diff --git a/modules/nf-core/pairtools/parse/meta.yml b/modules/nf-core/pairtools/parse/meta.yml
index 396fe795f0a..b8d0165e64d 100644
--- a/modules/nf-core/pairtools/parse/meta.yml
+++ b/modules/nf-core/pairtools/parse/meta.yml
@@ -2,6 +2,11 @@ name: pairtools_parse
 description: Find ligation junctions in .sam, make .pairs
 keywords:
   - parse
+  - ligations
+  - sam
+  - pairs
+  - Hi-C
+  - HiC
 tools:
   - pairtools:
       description: CLI tools to process mapped Hi-C data
diff --git a/modules/nf-core/pairtools/restrict/meta.yml b/modules/nf-core/pairtools/restrict/meta.yml
index 877335392a5..2a013effd77 100644
--- a/modules/nf-core/pairtools/restrict/meta.yml
+++ b/modules/nf-core/pairtools/restrict/meta.yml
@@ -2,6 +2,8 @@ name: pairtools_restrict
 description: Assign restriction fragments to pairs
 keywords:
   - sort
+  - pairs
+  - restriction fragments
 tools:
   - pairtools:
       description: CLI tools to process mapped Hi-C data
diff --git a/modules/nf-core/pairtools/select/meta.yml b/modules/nf-core/pairtools/select/meta.yml
index 47f4ce441a1..a5fd6218d1c 100644
--- a/modules/nf-core/pairtools/select/meta.yml
+++ b/modules/nf-core/pairtools/select/meta.yml
@@ -2,6 +2,8 @@ name: pairtools_select
 description: Select pairs according to given condition by options.args
 keywords:
   - select
+  - pairs
+  - pairtools
 tools:
   - pairtools:
       description: CLI tools to process mapped Hi-C data
diff --git a/modules/nf-core/panaroo/run/meta.yml b/modules/nf-core/panaroo/run/meta.yml
index 28ea310cffc..47655d218a9 100644
--- a/modules/nf-core/panaroo/run/meta.yml
+++ b/modules/nf-core/panaroo/run/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart"
       tool_dev_url: "https://github.com/gtonkinhill/panaroo"
       doi: "10.1186/s13059-020-02090-4"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml
index 5fd02c0b3b7..1ac43b7908e 100644
--- a/modules/nf-core/parabricks/applybqsr/meta.yml
+++ b/modules/nf-core/parabricks/applybqsr/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: "NVIDIA Clara Parabricks GPU-accelerated genomics tools"
       homepage: "https://www.nvidia.com/en-us/clara/genomics/"
       documentation: "https://docs.nvidia.com/clara/parabricks/"
-      licence: "custom"
+      licence: ["custom"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/paraclu/meta.yml b/modules/nf-core/paraclu/meta.yml
index 01ea897d47e..4307e68e272 100644
--- a/modules/nf-core/paraclu/meta.yml
+++ b/modules/nf-core/paraclu/meta.yml
@@ -2,6 +2,9 @@ name: paraclu
 description: Paraclu finds clusters in data attached to sequences.
 keywords:
   - sort
+  - cluster
+  - transcripts
+  - transcription start site
 tools:
   - paraclu:
       description: Paraclu finds clusters in data attached to sequences.
diff --git a/modules/nf-core/paragraph/idxdepth/meta.yml b/modules/nf-core/paragraph/idxdepth/meta.yml
index 042e5f8a944..19e90df24b8 100644
--- a/modules/nf-core/paragraph/idxdepth/meta.yml
+++ b/modules/nf-core/paragraph/idxdepth/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/Illumina/paragraph"
       tool_dev_url: "https://github.com/Illumina/paragraph"
       doi: "10.1101/635011"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/paragraph/multigrmpy/meta.yml b/modules/nf-core/paragraph/multigrmpy/meta.yml
index 84b435b75d4..56075bbf1da 100644
--- a/modules/nf-core/paragraph/multigrmpy/meta.yml
+++ b/modules/nf-core/paragraph/multigrmpy/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/Illumina/paragraph"
       tool_dev_url: "https://github.com/Illumina/paragraph"
       doi: "10.1101/635011"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/paragraph/vcf2paragraph/meta.yml b/modules/nf-core/paragraph/vcf2paragraph/meta.yml
index ab40b5023e5..c60991218c9 100644
--- a/modules/nf-core/paragraph/vcf2paragraph/meta.yml
+++ b/modules/nf-core/paragraph/vcf2paragraph/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/Illumina/paragraph"
       tool_dev_url: "https://github.com/Illumina/paragraph"
       doi: "10.1101/635011"
-      licence: "['Apache License 2.0']"
+      licence: ["Apache License 2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pasty/meta.yml b/modules/nf-core/pasty/meta.yml
index 9387549b852..8f7de15f429 100644
--- a/modules/nf-core/pasty/meta.yml
+++ b/modules/nf-core/pasty/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/rpetit3/pasty"
       documentation: "https://github.com/rpetit3/pasty"
       tool_dev_url: "https://github.com/rpetit3/pasty"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pbbam/pbmerge/meta.yml b/modules/nf-core/pbbam/pbmerge/meta.yml
index 016f362f4c0..9ad84d70dcd 100644
--- a/modules/nf-core/pbbam/pbmerge/meta.yml
+++ b/modules/nf-core/pbbam/pbmerge/meta.yml
@@ -2,7 +2,8 @@ name: pbbam_pbmerge
 description: The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
 keywords:
   - pbbam
-  - pbbam/pbmerge
+  - pbmerge
+  - pacbio
 tools:
   - pbbam:
       description: PacBio BAM C++ library
diff --git a/modules/nf-core/pbptyper/meta.yml b/modules/nf-core/pbptyper/meta.yml
index 648f71d439d..c12086adbd2 100644
--- a/modules/nf-core/pbptyper/meta.yml
+++ b/modules/nf-core/pbptyper/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/rpetit3/pbptyper"
       documentation: "https://github.com/rpetit3/pbptyper"
       tool_dev_url: "https://github.com/rpetit3/pbptyper"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pear/meta.yml b/modules/nf-core/pear/meta.yml
index 1b25bc08b4c..8f100600364 100644
--- a/modules/nf-core/pear/meta.yml
+++ b/modules/nf-core/pear/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "paired-end read merger"
       homepage: "https://cme.h-its.org/exelixis/web/software/pear/"
       documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html"
-      licence: "['Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported']"
+      licence: ["Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/peka/meta.yml b/modules/nf-core/peka/meta.yml
index a75764a1189..6c1adf1db1f 100644
--- a/modules/nf-core/peka/meta.yml
+++ b/modules/nf-core/peka/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/ulelab/peka"
       tool_dev_url: "https://github.com/ulelab/peka"
       doi: "10.1186/s13059-022-02755-2"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml
index 79899023e9f..276f6fddf6f 100644
--- a/modules/nf-core/phantompeakqualtools/meta.yml
+++ b/modules/nf-core/phantompeakqualtools/meta.yml
@@ -18,7 +18,7 @@ tools:
       documentation: "https://github.com/kundajelab/phantompeakqualtools"
       tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools"
       doi: "10.1101/gr.136184.111"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/phispy/meta.yml b/modules/nf-core/phispy/meta.yml
index 49017252a9a..e066a58b18a 100644
--- a/modules/nf-core/phispy/meta.yml
+++ b/modules/nf-core/phispy/meta.yml
@@ -16,7 +16,7 @@ tools:
       documentation: "https://github.com/linsalrob/PhiSpy/blob/master/README.md"
       tool_dev_url: "https://github.com/linsalrob/PhiSpy/"
       doi: "10.1093/nar/gks406"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pilon/meta.yml b/modules/nf-core/pilon/meta.yml
index 6a395a204e2..a54bd254f4c 100644
--- a/modules/nf-core/pilon/meta.yml
+++ b/modules/nf-core/pilon/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
       tool_dev_url: "https://github.com/broadinstitute/pilon"
       doi: "10.1371/journal.pone.0112963"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pindel/pindel/meta.yml b/modules/nf-core/pindel/pindel/meta.yml
index df5d0a68aaf..6b44f78e150 100755
--- a/modules/nf-core/pindel/pindel/meta.yml
+++ b/modules/nf-core/pindel/pindel/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data"
       homepage: "https://gmt.genome.wustl.edu/packages/pindel/"
       documentation: https://gmt.genome.wustl.edu/packages/pindel/user-manual.html
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pints/caller/meta.yml b/modules/nf-core/pints/caller/meta.yml
index 020609f1788..a0df262997a 100644
--- a/modules/nf-core/pints/caller/meta.yml
+++ b/modules/nf-core/pints/caller/meta.yml
@@ -19,7 +19,7 @@ tools:
       documentation: "https://github.com/hyulab/PINTS/blob/main/README.md"
       tool_dev_url: "https://github.com/hyulab/PINTS"
       doi: "10.1038/s41587-022-01211-7"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/plasmidfinder/meta.yml b/modules/nf-core/plasmidfinder/meta.yml
index 37b6e296789..946d29f0741 100644
--- a/modules/nf-core/plasmidfinder/meta.yml
+++ b/modules/nf-core/plasmidfinder/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
       tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder"
       doi: "10.1128/AAC.02412-14"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/platypus/meta.yml b/modules/nf-core/platypus/meta.yml
index 8f8749ce0f1..9b9a83a0194 100644
--- a/modules/nf-core/platypus/meta.yml
+++ b/modules/nf-core/platypus/meta.yml
@@ -3,6 +3,7 @@ description: Platypus is a tool that efficiently and accurately calling genetic
 keywords:
   - variant calling
   - dna sequencing
+  - vcf
 tools:
   - platypus:
       description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.
diff --git a/modules/nf-core/plink/extract/meta.yml b/modules/nf-core/plink/extract/meta.yml
index b4cd092640d..cd4cfc12765 100644
--- a/modules/nf-core/plink/extract/meta.yml
+++ b/modules/nf-core/plink/extract/meta.yml
@@ -3,6 +3,7 @@ description: Subset plink bfiles with a text file of variant identifiers
 keywords:
   - extract
   - plink
+  - Whole genome association analysis
 tools:
   - plink:
       description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
diff --git a/modules/nf-core/plink/indeppairwise/meta.yml b/modules/nf-core/plink/indeppairwise/meta.yml
index c77a79bc248..531afd12aae 100644
--- a/modules/nf-core/plink/indeppairwise/meta.yml
+++ b/modules/nf-core/plink/indeppairwise/meta.yml
@@ -32,15 +32,15 @@ input:
       description: PLINK sample information file
       pattern: "*.{fam}"
   - window_size:
-      type: number
+      type: integer
       description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold.
       pattern: "*.{}"
   - variant_count:
-      type: number
+      type: integer
       description: Variant count to shift the window at the end of each step.
       pattern: "*.{}"
   - r2_threshold:
-      type: number
+      type: integer
       description: Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain
       pattern: "*.{}"
 output:
diff --git a/modules/nf-core/plink/recode/meta.yml b/modules/nf-core/plink/recode/meta.yml
index 057878b4c47..5c0e0f08f16 100644
--- a/modules/nf-core/plink/recode/meta.yml
+++ b/modules/nf-core/plink/recode/meta.yml
@@ -2,13 +2,16 @@ name: "plink_recode"
 description: Recodes plink bfiles into a new text fileset applying different modifiers
 keywords:
   - recode
+  - plink
+  - Whole genome association analysis
+  - WGAA
 tools:
   - "plink":
       description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner."
       homepage: "https://www.cog-genomics.org/plink"
       documentation: "https://www.cog-genomics.org/plink/1.9/data#recode"
       tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/plink/vcf/meta.yml b/modules/nf-core/plink/vcf/meta.yml
index 541b2c72f0b..79ddde27a0e 100644
--- a/modules/nf-core/plink/vcf/meta.yml
+++ b/modules/nf-core/plink/vcf/meta.yml
@@ -3,6 +3,7 @@ description: Analyses variant calling files using plink
 keywords:
   - plink
   - vcf
+  - Whole genome association analysis
 tools:
   - plink:
       description: |
diff --git a/modules/nf-core/pneumocat/meta.yml b/modules/nf-core/pneumocat/meta.yml
index 0a7124639cd..8015826add9 100644
--- a/modules/nf-core/pneumocat/meta.yml
+++ b/modules/nf-core/pneumocat/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/ukhsa-collaboration/PneumoCaT"
       tool_dev_url: "https://github.com/ukhsa-collaboration/PneumoCaT"
       doi: "10.7717/peerj.2477"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml
index 67d9ff486d5..4fd9795408a 100644
--- a/modules/nf-core/porechop/abi/meta.yml
+++ b/modules/nf-core/porechop/abi/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/bonsai-team/Porechop_ABI"
       tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI"
       doi: "10.1101/2022.07.07.499093"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/prinseqplusplus/meta.yml b/modules/nf-core/prinseqplusplus/meta.yml
index ca8542ff649..a978be4a5cd 100644
--- a/modules/nf-core/prinseqplusplus/meta.yml
+++ b/modules/nf-core/prinseqplusplus/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
       tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
       doi: "10.7287/peerj.preprints.27553v1"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/proteus/readproteingroups/meta.yml b/modules/nf-core/proteus/readproteingroups/meta.yml
index 8034770a0de..4e67cf0c289 100644
--- a/modules/nf-core/proteus/readproteingroups/meta.yml
+++ b/modules/nf-core/proteus/readproteingroups/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://rdrr.io/github/bartongroup/Proteus/"
       tool_dev_url: "https://github.com/bartongroup/Proteus"
       doi: "10.1101/416511"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/pureclip/meta.yml b/modules/nf-core/pureclip/meta.yml
index 4f5b53cdc36..48308ce6344 100644
--- a/modules/nf-core/pureclip/meta.yml
+++ b/modules/nf-core/pureclip/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://pureclip.readthedocs.io/en/latest/GettingStarted/index.html"
       tool_dev_url: "https://github.com/skrakau/PureCLIP"
       doi: "10.1186/s13059-017-1364-2"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/purecn/coverage/meta.yml b/modules/nf-core/purecn/coverage/meta.yml
index c18f08f9fba..4663187ad73 100644
--- a/modules/nf-core/purecn/coverage/meta.yml
+++ b/modules/nf-core/purecn/coverage/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html"
       tool_dev_url: "https://github.com/lima1/PureCN"
       doi: "10.1186/s13029-016-0060-z"
-      licence: "Artistic-2.0"
+      licence: ["Artistic-2.0"]
       args_id: "$args"
 input:
   - meta:
diff --git a/modules/nf-core/purecn/intervalfile/meta.yml b/modules/nf-core/purecn/intervalfile/meta.yml
index 51f5b3a6b7b..b2dc3899606 100644
--- a/modules/nf-core/purecn/intervalfile/meta.yml
+++ b/modules/nf-core/purecn/intervalfile/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html"
       tool_dev_url: "https://github.com/lima1/PureCN"
       doi: "10.1186/s13029-016-0060-z."
-      licence: "Artistic-2.0"
+      licence: ["Artistic-2.0"]
       args_id: "$args"
 input:
   - meta:
diff --git a/modules/nf-core/purecn/normaldb/meta.yml b/modules/nf-core/purecn/normaldb/meta.yml
index 4188f17a86d..cddabe9f0e1 100644
--- a/modules/nf-core/purecn/normaldb/meta.yml
+++ b/modules/nf-core/purecn/normaldb/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html"
       tool_dev_url: "https://github.com/lima1/PureCN"
       doi: "10.1186/s13029-016-0060-z"
-      licence: "Artistic-2.0"
+      licence: ["Artistic-2.0"]
       args_id: "$args"
 input:
   - meta:
diff --git a/modules/nf-core/purecn/run/meta.yml b/modules/nf-core/purecn/run/meta.yml
index afbe9532523..23da25e6779 100644
--- a/modules/nf-core/purecn/run/meta.yml
+++ b/modules/nf-core/purecn/run/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html"
       tool_dev_url: "https://github.com/lima1/PureCN"
       doi: "10.1186/s13029-016-0060-z"
-      licence: "Artistic-2.0"
+      licence: ["Artistic-2.0"]
       args_id: "$args"
 input:
   - meta:
diff --git a/modules/nf-core/purgedups/getseqs/meta.yml b/modules/nf-core/purgedups/getseqs/meta.yml
index e581b8a470c..2b759ce4f02 100644
--- a/modules/nf-core/purgedups/getseqs/meta.yml
+++ b/modules/nf-core/purgedups/getseqs/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/dfguan/purge_dups"
       tool_dev_url: "https://github.com/dfguan/purge_dups"
       doi: "10.1093/bioinformatics/btaa025"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/purgedups/histplot/meta.yml b/modules/nf-core/purgedups/histplot/meta.yml
index bfd5a0d4a73..47596104f21 100644
--- a/modules/nf-core/purgedups/histplot/meta.yml
+++ b/modules/nf-core/purgedups/histplot/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/dfguan/purge_dups"
       tool_dev_url: "https://github.com/dfguan/purge_dups"
       doi: "10.1093/bioinformatics/btaa025"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/purgedups/pbcstat/meta.yml b/modules/nf-core/purgedups/pbcstat/meta.yml
index ffbef6e7cd6..875de168cf8 100644
--- a/modules/nf-core/purgedups/pbcstat/meta.yml
+++ b/modules/nf-core/purgedups/pbcstat/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/dfguan/purge_dups"
       tool_dev_url: "https://github.com/dfguan/purge_dups"
       doi: "10.1093/bioinformatics/btaa025"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/purgedups/splitfa/meta.yml b/modules/nf-core/purgedups/splitfa/meta.yml
index 2b1fa3c4985..d1fd37e12a8 100644
--- a/modules/nf-core/purgedups/splitfa/meta.yml
+++ b/modules/nf-core/purgedups/splitfa/meta.yml
@@ -3,6 +3,8 @@ description: Split fasta file by 'N's to aid in self alignment for duplicate pur
 keywords:
   - split assembly
   - duplicate purging
+  - self alignment
+  - fasta
 tools:
   - "purgedups":
       description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth"
@@ -10,7 +12,7 @@ tools:
       documentation: "https://github.com/dfguan/purge_dups"
       tool_dev_url: "https://github.com/dfguan/purge_dups"
       doi: "10.1093/bioinformatics/btaa025"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/qcat/meta.yml b/modules/nf-core/qcat/meta.yml
index 8d7274680a0..833176f4591 100644
--- a/modules/nf-core/qcat/meta.yml
+++ b/modules/nf-core/qcat/meta.yml
@@ -2,6 +2,8 @@ name: qcat
 description: Demultiplexer for Nanopore samples
 keywords:
   - demultiplex
+  - nanopore
+  - ONT
 tools:
   - qcat:
       description: |
diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml
index 34c67a79db7..02d418d3cf2 100644
--- a/modules/nf-core/quilt/quilt/meta.yml
+++ b/modules/nf-core/quilt/quilt/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/rwdavies/quilt"
       tool_dev_url: "https://github.com/rwdavies/quilt"
       doi: "10.1038/s41588-021-00877-0"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml
index ecc8e1e43a9..09a64d2591f 100644
--- a/modules/nf-core/rhocall/annotate/meta.yml
+++ b/modules/nf-core/rhocall/annotate/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/dnil/rhocall"
       documentation: "https://github.com/dnil/rhocall"
       tool_dev_url: "https://github.com/dnil"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml
index f84f068216a..379690f7528 100644
--- a/modules/nf-core/rmarkdownnotebook/meta.yml
+++ b/modules/nf-core/rmarkdownnotebook/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: https://rmarkdown.rstudio.com/
       documentation: https://rmarkdown.rstudio.com/lesson-1.html
       tool_dev_url: https://github.com/rstudio/rmarkdown
-      licence: GPL-3
+      licence: ["GPL-3"]
 params:
   - parametrize:
       type: boolean
diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml
index 8ed18f5407d..1991b807d01 100644
--- a/modules/nf-core/rtgtools/format/meta.yml
+++ b/modules/nf-core/rtgtools/format/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://www.realtimegenomics.com/products/rtg-tools"
       documentation: "https://github.com/RealTimeGenomics/rtg-tools"
       tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/rtgtools/pedfilter/meta.yml b/modules/nf-core/rtgtools/pedfilter/meta.yml
index 785ac99040a..4e90fd7bf98 100644
--- a/modules/nf-core/rtgtools/pedfilter/meta.yml
+++ b/modules/nf-core/rtgtools/pedfilter/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.realtimegenomics.com/products/rtg-tools"
       documentation: "https://github.com/RealTimeGenomics/rtg-tools"
       tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml
index 927cff90c35..2b4d43d7c91 100644
--- a/modules/nf-core/rtgtools/rocplot/meta.yml
+++ b/modules/nf-core/rtgtools/rocplot/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.realtimegenomics.com/products/rtg-tools"
       documentation: "https://github.com/RealTimeGenomics/rtg-tools"
       tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml
index f67a35c0dbf..5023ac91822 100644
--- a/modules/nf-core/rtgtools/vcfeval/meta.yml
+++ b/modules/nf-core/rtgtools/vcfeval/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://www.realtimegenomics.com/products/rtg-tools"
       documentation: "https://github.com/RealTimeGenomics/rtg-tools"
       tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/salsa2/meta.yml b/modules/nf-core/salsa2/meta.yml
index e9ba0efe739..8729ce06443 100644
--- a/modules/nf-core/salsa2/meta.yml
+++ b/modules/nf-core/salsa2/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/marbl/SALSA"
       tool_dev_url: "https://github.com/marbl/SALSA"
       doi: "10.1186/s12864-017-3879-z"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sam2lca/analyze/meta.yml b/modules/nf-core/sam2lca/analyze/meta.yml
index 176122eb95b..aa4f9e310d9 100644
--- a/modules/nf-core/sam2lca/analyze/meta.yml
+++ b/modules/nf-core/sam2lca/analyze/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://github.com/maxibor/sam2lca"
       documentation: "https://sam2lca.readthedocs.io"
       doi: "10.21105/joss.04360"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sambamba/flagstat/meta.yml b/modules/nf-core/sambamba/flagstat/meta.yml
index 0ab9de636d5..3e68823a5c7 100644
--- a/modules/nf-core/sambamba/flagstat/meta.yml
+++ b/modules/nf-core/sambamba/flagstat/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html"
       documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html"
       tool_dev_url: "https://github.com/biod/sambamba"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sambamba/markdup/meta.yml b/modules/nf-core/sambamba/markdup/meta.yml
index bf7d210770e..51d66ecade4 100644
--- a/modules/nf-core/sambamba/markdup/meta.yml
+++ b/modules/nf-core/sambamba/markdup/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html"
       documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html"
       tool_dev_url: "https://github.com/biod/sambamba"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/scimap/mcmicro/meta.yml b/modules/nf-core/scimap/mcmicro/meta.yml
index 36920763bd6..3c517372c15 100644
--- a/modules/nf-core/scimap/mcmicro/meta.yml
+++ b/modules/nf-core/scimap/mcmicro/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://scimap.xyz/"
       documentation: "https://scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap/"
       tool_dev_url: "https://github.com/labsyspharm/scimap"
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   # Only when we have meta
   - meta:
diff --git a/modules/nf-core/scramble/clusteranalysis/meta.yml b/modules/nf-core/scramble/clusteranalysis/meta.yml
index d60e9dc96cf..f5c934847df 100644
--- a/modules/nf-core/scramble/clusteranalysis/meta.yml
+++ b/modules/nf-core/scramble/clusteranalysis/meta.yml
@@ -3,13 +3,14 @@ description: The Cluster Analysis tool of Scramble analyses and interprets the s
 keywords:
   - soft-clipped clusters
   - scramble
+  - cluster analysis
 tools:
   - "scramble":
       description: "Soft Clipped Read Alignment Mapper"
       homepage: "https://github.com/GeneDx/scramble"
       documentation: "https://github.com/GeneDx/scramble"
       tool_dev_url: "https://github.com/GeneDx/scramble"
-      licence: "['CC']"
+      licence: ["CC"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/scramble/clusteridentifier/meta.yml b/modules/nf-core/scramble/clusteridentifier/meta.yml
index 94d743b3b72..17aab2c08a8 100644
--- a/modules/nf-core/scramble/clusteridentifier/meta.yml
+++ b/modules/nf-core/scramble/clusteridentifier/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/GeneDx/scramble"
       documentation: "https://github.com/GeneDx/scramble"
       tool_dev_url: "https://github.com/GeneDx/scramble"
-      licence: "['CC']"
+      licence: ["CC"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml
index aaad17ebd71..95f5aa37d2f 100644
--- a/modules/nf-core/segemehl/align/meta.yml
+++ b/modules/nf-core/segemehl/align/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/"
       documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/"
       doi: "10.1186/gb-2014-15-2-r34"
-      licence: "GPL v3"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/segemehl/index/meta.yml b/modules/nf-core/segemehl/index/meta.yml
index f2b9eb2259f..a036602da95 100644
--- a/modules/nf-core/segemehl/index/meta.yml
+++ b/modules/nf-core/segemehl/index/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/"
       documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/"
       doi: "10.1186/gb-2014-15-2-r34"
-      licence: "GPL v3"
+      licence: ["GPL v3"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/semibin/singleeasybin/meta.yml b/modules/nf-core/semibin/singleeasybin/meta.yml
index f752fe6ff15..9e7c491a461 100644
--- a/modules/nf-core/semibin/singleeasybin/meta.yml
+++ b/modules/nf-core/semibin/singleeasybin/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://semibin.readthedocs.io/en/latest/"
       tool_dev_url: "https://github.com/BigDataBiology/SemiBin"
       doi: "10.1038/s41467-022-29843-y"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/seqkit/pair/meta.yml b/modules/nf-core/seqkit/pair/meta.yml
index 5eecd01b50a..4a49926ae92 100644
--- a/modules/nf-core/seqkit/pair/meta.yml
+++ b/modules/nf-core/seqkit/pair/meta.yml
@@ -3,6 +3,7 @@ description: match up paired-end reads from two fastq files
 keywords:
   - seqkit
   - pair
+  - fastq
 tools:
   - seqkit:
       description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml
index 1d69d28b78e..cdfb82cd1ec 100644
--- a/modules/nf-core/seqkit/replace/meta.yml
+++ b/modules/nf-core/seqkit/replace/meta.yml
@@ -3,6 +3,8 @@ description: Use seqkit to find/replace strings within sequences and sequence he
 keywords:
   - seqkit
   - replace
+  - find
+  - sequence headers
 tools:
   - seqkit:
       description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml
index e23b1342616..14babd448b6 100644
--- a/modules/nf-core/seqkit/split2/meta.yml
+++ b/modules/nf-core/seqkit/split2/meta.yml
@@ -3,6 +3,7 @@ description: Split single or paired-end fastq.gz files
 keywords:
   - split
   - fastq
+  - seqkit
 tools:
   - seqkit:
       description: |
diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml
index 2d51c68dcea..ab1d5ef9af8 100644
--- a/modules/nf-core/seqkit/stats/meta.yml
+++ b/modules/nf-core/seqkit/stats/meta.yml
@@ -3,6 +3,8 @@ description: simple statistics of FASTA/Q files
 keywords:
   - seqkit
   - stats
+  - fasta
+  - fastq
 tools:
   - "seqkit":
       description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
diff --git a/modules/nf-core/seqtk/mergepe/meta.yml b/modules/nf-core/seqtk/mergepe/meta.yml
index 80df9e78e8e..89afbe4ff0b 100644
--- a/modules/nf-core/seqtk/mergepe/meta.yml
+++ b/modules/nf-core/seqtk/mergepe/meta.yml
@@ -2,6 +2,8 @@ name: seqtk_mergepe
 description: Interleave pair-end reads from FastQ files
 keywords:
   - interleave
+  - fastq
+  - pair-end
 tools:
   - seqtk:
       description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
diff --git a/modules/nf-core/seqtk/rename/meta.yml b/modules/nf-core/seqtk/rename/meta.yml
index de5f393cca9..5de7d68e5f6 100644
--- a/modules/nf-core/seqtk/rename/meta.yml
+++ b/modules/nf-core/seqtk/rename/meta.yml
@@ -2,6 +2,8 @@ name: seqtk_rename
 description: Rename sequence names in FASTQ or FASTA files.
 keywords:
   - rename
+  - fastq
+  - fasta
 tools:
   - seqtk:
       description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names.
diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml
index 549aee9c282..853597fc3db 100644
--- a/modules/nf-core/seqtk/sample/meta.yml
+++ b/modules/nf-core/seqtk/sample/meta.yml
@@ -2,6 +2,8 @@ name: seqtk_sample
 description: Subsample reads from FASTQ files
 keywords:
   - sample
+  - fastq
+  - subsample
 tools:
   - seqtk:
       description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences.
@@ -20,7 +22,7 @@ input:
       description: List of input FastQ files
       pattern: "*.{fastq.gz}"
   - sample_size:
-      type: value
+      type: integer
       description: Number of reads to sample.
 output:
   - meta:
diff --git a/modules/nf-core/seqtk/subseq/meta.yml b/modules/nf-core/seqtk/subseq/meta.yml
index 2cb8858d5ab..87d2e6428b8 100644
--- a/modules/nf-core/seqtk/subseq/meta.yml
+++ b/modules/nf-core/seqtk/subseq/meta.yml
@@ -1,7 +1,11 @@
 name: seqtk_subseq
 description: Select only sequences that match the filtering condition
 keywords:
-  - filtering,selection
+  - filtering
+  - selection
+  - sequence
+  - fasta
+  - fastq
 tools:
   - seqtk:
       description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
diff --git a/modules/nf-core/sequencetools/pileupcaller/meta.yml b/modules/nf-core/sequencetools/pileupcaller/meta.yml
index 54ed15b0f2e..ae95ce5df4a 100644
--- a/modules/nf-core/sequencetools/pileupcaller/meta.yml
+++ b/modules/nf-core/sequencetools/pileupcaller/meta.yml
@@ -16,7 +16,7 @@ tools:
       homepage: "https://github.com/stschiff/sequenceTools"
       documentation: "https://github.com/stschiff/sequenceTools#readme"
       tool_dev_url: "https://github.com/stschiff/sequenceTools"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta:
@@ -33,11 +33,13 @@ input:
         Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on.
         Only alleles matching the Ref and Alt alleles of the provided snp file will be called.
   - calling_method:
-      type: value
+      type: string
       description: The desired calling method for pileupcaller. One of 'randomHaploid', 'randomDiploid', or 'majorityCall'.
+      pattern: "randomHaploid|randomDiploid|majorityCall"
   - output_format:
-      type: value
+      type: string
       description: The desired output format. One of 'PLINK', 'EIGENSTRAT', or 'FREQSUM'.
+      pattern: "PLINK|EIGENSTRAT|FREQSUM"
 output:
   #Only when we have meta
   - meta:
diff --git a/modules/nf-core/seroba/run/meta.yml b/modules/nf-core/seroba/run/meta.yml
index 08ff448cec8..e0a704ccc22 100644
--- a/modules/nf-core/seroba/run/meta.yml
+++ b/modules/nf-core/seroba/run/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://sanger-pathogens.github.io/seroba/"
       tool_dev_url: "https://github.com/sanger-pathogens/seroba"
       doi: "10.1099/mgen.0.000186"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sexdeterrmine/meta.yml b/modules/nf-core/sexdeterrmine/meta.yml
index 1c4b33b1fd2..f1b57a8f3ec 100644
--- a/modules/nf-core/sexdeterrmine/meta.yml
+++ b/modules/nf-core/sexdeterrmine/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
       tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
       doi: "10.1038/s41467-018-07483-5"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml
index ab68274eb89..19357ee77d0 100644
--- a/modules/nf-core/shapeit5/ligate/meta.yml
+++ b/modules/nf-core/shapeit5/ligate/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
       doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shapeit5/phasecommon/meta.yml b/modules/nf-core/shapeit5/phasecommon/meta.yml
index 5d1381fba5b..47197291ea9 100644
--- a/modules/nf-core/shapeit5/phasecommon/meta.yml
+++ b/modules/nf-core/shapeit5/phasecommon/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
       doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shapeit5/phaserare/meta.yml b/modules/nf-core/shapeit5/phaserare/meta.yml
index b607053d732..dbc0aa13d03 100644
--- a/modules/nf-core/shapeit5/phaserare/meta.yml
+++ b/modules/nf-core/shapeit5/phaserare/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
       doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      licence: ["MIT"]
 requirement: AVX2
 input:
   - meta:
diff --git a/modules/nf-core/shapeit5/switch/meta.yml b/modules/nf-core/shapeit5/switch/meta.yml
index 9832e8166bb..73dd86e49d4 100644
--- a/modules/nf-core/shapeit5/switch/meta.yml
+++ b/modules/nf-core/shapeit5/switch/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
       doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml
index d8f037009f7..2694db9868a 100644
--- a/modules/nf-core/shasum/meta.yml
+++ b/modules/nf-core/shasum/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: Create an SHA256 (256-bit) checksum.
       homepage: "https://www.gnu.org"
       documentation: "https://linux.die.net/man/1/shasum"
-      licence: GPLv3+
+      licence: ["GPLv3+"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shigatyper/meta.yml b/modules/nf-core/shigatyper/meta.yml
index f7a7fd7aee9..65e1de01890 100644
--- a/modules/nf-core/shigatyper/meta.yml
+++ b/modules/nf-core/shigatyper/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/CFSAN-Biostatistics/shigatyper"
       tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper"
       doi: "10.1128/AEM.00165-19"
-      licence: "['Public Domain']"
+      licence: ["Public Domain"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/shigeifinder/meta.yml b/modules/nf-core/shigeifinder/meta.yml
index 9096affa2ed..8951b5299b6 100644
--- a/modules/nf-core/shigeifinder/meta.yml
+++ b/modules/nf-core/shigeifinder/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/LanLab/ShigEiFinder"
       tool_dev_url: "https://github.com/LanLab/ShigEiFinder"
       doi: "10.1099/mgen.0.000704"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sickle/meta.yml b/modules/nf-core/sickle/meta.yml
index 76bc07c1c3c..da94c23d6f6 100644
--- a/modules/nf-core/sickle/meta.yml
+++ b/modules/nf-core/sickle/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "a tool that determines clipping of reads on 3' end and 5'end based on base quality "
       homepage: "https://github.com/najoshi/sickle"
       tool_dev_url: "https://github.com/najoshi/sickle"
-      licence: "['MIT License']"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/slimfastq/meta.yml b/modules/nf-core/slimfastq/meta.yml
index b5f3d8d8e67..72036d89829 100644
--- a/modules/nf-core/slimfastq/meta.yml
+++ b/modules/nf-core/slimfastq/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: "slimfastq efficiently compresses/decompresses FASTQ files"
       homepage: "https://github.com/Infinidat/slimfastq"
       tool_dev_url: "https://github.com/Infinidat/slimfastq"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/smncopynumbercaller/meta.yml b/modules/nf-core/smncopynumbercaller/meta.yml
index bb2690e978a..f318a2b7a34 100644
--- a/modules/nf-core/smncopynumbercaller/meta.yml
+++ b/modules/nf-core/smncopynumbercaller/meta.yml
@@ -1,7 +1,11 @@
 name: "smncopynumbercaller"
 description: tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
 keywords:
-  - copy number, BAM, CRAM, SMN1, SMN2
+  - copy number
+  - BAM
+  - CRAM
+  - SMN1
+  - SMN2
 tools:
   - "smncopynumbercaller":
       description: "call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file"
@@ -9,7 +13,7 @@ tools:
       documentation: "https://github.com/Illumina/SMNCopyNumberCaller"
       tool_dev_url: "https://github.com/Illumina/SMNCopyNumberCaller"
       doi: "10.1038/s41436-020-0754-0"
-      licence: "Apache License Version 2.0"
+      licence: ["Apache License Version 2.0"]
 input:
   - bam:
       type: file
diff --git a/modules/nf-core/smoove/call/meta.yml b/modules/nf-core/smoove/call/meta.yml
index 1b8280ab691..bff9916b96f 100644
--- a/modules/nf-core/smoove/call/meta.yml
+++ b/modules/nf-core/smoove/call/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: https://github.com/brentp/smoove
       documentation: https://brentp.github.io/post/smoove/
       tool_dev_url: https://github.com/brentp/smoove
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/snakemake/meta.yml b/modules/nf-core/snakemake/meta.yml
index efbe01d2adf..3da2765988e 100644
--- a/modules/nf-core/snakemake/meta.yml
+++ b/modules/nf-core/snakemake/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://snakemake.readthedocs.io/en/stable/"
       tool_dev_url: "https://github.com/snakemake/snakemake"
       doi: "10.1093/bioinformatics/bty350"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta:
diff --git a/modules/nf-core/snapaligner/align/meta.yml b/modules/nf-core/snapaligner/align/meta.yml
index 16e2a5e6f10..137b67e18ab 100644
--- a/modules/nf-core/snapaligner/align/meta.yml
+++ b/modules/nf-core/snapaligner/align/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
       tool_dev_url: "https://github.com/amplab/snap"
       doi: "10.1101/2021.11.23.469039"
-      licence: "['Apache v2']"
+      licence: ["Apache v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/snapaligner/index/meta.yml b/modules/nf-core/snapaligner/index/meta.yml
index f8c84c38b73..bf84a6b78ff 100644
--- a/modules/nf-core/snapaligner/index/meta.yml
+++ b/modules/nf-core/snapaligner/index/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
       tool_dev_url: "https://github.com/amplab/snap"
       doi: "10.1101/2021.11.23.469039"
-      licence: "['Apache v2']"
+      licence: ["Apache v2"]
 input:
   - meta2:
       type: map
diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml
index 4b246965877..1fe053c1608 100644
--- a/modules/nf-core/sniffles/meta.yml
+++ b/modules/nf-core/sniffles/meta.yml
@@ -3,6 +3,8 @@ description: structural-variant calling with sniffles
 keywords:
   - sniffles
   - structural-variant calling
+  - long-read sequencing
+  - SVC
 tools:
   - sniffles:
       description: a fast structural variant caller for long-read sequencing
diff --git a/modules/nf-core/snippy/core/meta.yml b/modules/nf-core/snippy/core/meta.yml
index afb245c7432..cd548b67ed4 100644
--- a/modules/nf-core/snippy/core/meta.yml
+++ b/modules/nf-core/snippy/core/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/tseemann/snippy"
       documentation: "https://github.com/tseemann/snippy"
       tool_dev_url: "https://github.com/tseemann/snippy"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/snippy/run/meta.yml b/modules/nf-core/snippy/run/meta.yml
index 0daf05a8180..e5fafb2f461 100644
--- a/modules/nf-core/snippy/run/meta.yml
+++ b/modules/nf-core/snippy/run/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/tseemann/snippy"
       documentation: "https://github.com/tseemann/snippy"
       tool_dev_url: "https://github.com/tseemann/snippy"
-      licence: "['GPL v2']"
+      licence: ["GPL v2"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/snpdists/meta.yml b/modules/nf-core/snpdists/meta.yml
index 9266effbb75..82947744440 100644
--- a/modules/nf-core/snpdists/meta.yml
+++ b/modules/nf-core/snpdists/meta.yml
@@ -1,8 +1,9 @@
 name: snpdists
 description: Pairwise SNP distance matrix from a FASTA sequence alignment
 keywords:
-  - snp-dists
-  - distance-matrix
+  - snp distance
+  - distance matrix
+  - fasta
 tools:
   - snpdists:
       description: Convert a FASTA alignment to SNP distance matrix
diff --git a/modules/nf-core/snpsift/split/meta.yml b/modules/nf-core/snpsift/split/meta.yml
index a98e68f5f66..728ccd79b73 100644
--- a/modules/nf-core/snpsift/split/meta.yml
+++ b/modules/nf-core/snpsift/split/meta.yml
@@ -19,8 +19,8 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcf:
-      type: file (split) or list of files (join)
-      description: VCF file(s)
+      type: file
+      description: VCF file(s), either one (split) or list of files (join)
       pattern: "*.{vcf,vcf.gz}"
 output:
   - meta:
diff --git a/modules/nf-core/somalier/ancestry/meta.yml b/modules/nf-core/somalier/ancestry/meta.yml
index 0aadac517b4..6cc67ba6d6e 100644
--- a/modules/nf-core/somalier/ancestry/meta.yml
+++ b/modules/nf-core/somalier/ancestry/meta.yml
@@ -19,7 +19,7 @@ tools:
       documentation: "https://github.com/brentp/somalier"
       tool_dev_url: "https://github.com/brentp/somalier"
       doi: "10.1186/s13073-020-00761-2"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml
index 7aa426ab9ed..ecad228864e 100644
--- a/modules/nf-core/somalier/extract/meta.yml
+++ b/modules/nf-core/somalier/extract/meta.yml
@@ -19,7 +19,7 @@ tools:
       documentation: "https://github.com/brentp/somalier/blob/master/README.md"
       tool_dev_url: "https://github.com/brentp/somalier"
       doi: "10.1186/s13073-020-00761-2"
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml
index d1d81c872a5..4b192de98c1 100644
--- a/modules/nf-core/somalier/relate/meta.yml
+++ b/modules/nf-core/somalier/relate/meta.yml
@@ -19,7 +19,7 @@ tools:
       documentation: "https://github.com/brentp/somalier/blob/master/README.md"
       tool_dev_url: "https://github.com/brentp/somalier"
       doi: "10.1186/s13073-020-00761-2"
-      licence: "MIT License"
+      licence: ["MIT License"]
 input:
   - meta:
       type: map
@@ -27,7 +27,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - extract:
-      type: file(s)
+      type: file
       description: extract file(s) from Somalier extract
       pattern: "*.somalier"
   - ped:
diff --git a/modules/nf-core/sourmash/compare/meta.yml b/modules/nf-core/sourmash/compare/meta.yml
index e69dfde8f6e..056179f74dd 100644
--- a/modules/nf-core/sourmash/compare/meta.yml
+++ b/modules/nf-core/sourmash/compare/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: "https://sourmash.readthedocs.io/"
       tool_dev_url: "https://github.com/sourmash-bio/sourmash"
       doi: "10.21105/joss.00027"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/sourmash/index/meta.yml b/modules/nf-core/sourmash/index/meta.yml
index 55898c30f95..2cf1bbd6c0c 100644
--- a/modules/nf-core/sourmash/index/meta.yml
+++ b/modules/nf-core/sourmash/index/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://sourmash.readthedocs.io/"
       tool_dev_url: "https://github.com/sourmash-bio/sourmash"
       doi: "10.21105/joss.00027"
-      licence: "['BSD-3-clause']"
+      licence: ["BSD-3-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml
index 167ac8c8851..7c3f8cb4a6b 100644
--- a/modules/nf-core/spaceranger/count/meta.yml
+++ b/modules/nf-core/spaceranger/count/meta.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "spaceranger_count"
-description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data
+description: Module to use the 10x Spaceranger pipeline to proces 10x spatial transcriptomics data
 keywords:
   - align
   - count
@@ -20,8 +20,7 @@ tools:
       homepage: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       documentation: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
-      licence:
-        - "10x Genomics EULA"
+      licence: ["10x Genomics EULA"]
 input:
   - meta:
       type: map
@@ -70,7 +69,7 @@ input:
       pattern: "*.json"
   - reference:
       type: directory
-      description: Folder containing all the reference indices needed by Space Ranger
+      description: Folder containing all the reference indices needed by Spaceranger
   - probeset:
       type: file
       description: OPTIONAL - Probe set specification.
@@ -83,8 +82,8 @@ output:
         e.g. [ id:'test', single_end:false ]
   - outs:
       type: file
-      description: Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list
-      pattern: "outs/*"
+      description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
+      pattern: "${meta.id}/outs/*"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/spaceranger/mkgtf/meta.yml b/modules/nf-core/spaceranger/mkgtf/meta.yml
index 125b12622ba..c64e5aa8dbe 100644
--- a/modules/nf-core/spaceranger/mkgtf/meta.yml
+++ b/modules/nf-core/spaceranger/mkgtf/meta.yml
@@ -1,7 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "spaceranger_mkgtf"
-description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.
+description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
 keywords:
   - reference
   - mkref
@@ -19,8 +19,7 @@ tools:
       homepage: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       documentation: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
-      licence:
-        - "10x Genomics EULA"
+      licence: ["10x Genomics EULA"]
 input:
   - gtf:
       type: file
diff --git a/modules/nf-core/spaceranger/mkref/meta.yml b/modules/nf-core/spaceranger/mkref/meta.yml
index 453a3e56cc6..3be4b02062d 100644
--- a/modules/nf-core/spaceranger/mkref/meta.yml
+++ b/modules/nf-core/spaceranger/mkref/meta.yml
@@ -19,8 +19,7 @@ tools:
       homepage: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       documentation: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
       tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger"
-      licence:
-        - "10x Genomics EULA"
+      licence: ["10x Genomics EULA"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/spatyper/meta.yml b/modules/nf-core/spatyper/meta.yml
index 73ffce6fb00..2af1abca8a5 100644
--- a/modules/nf-core/spatyper/meta.yml
+++ b/modules/nf-core/spatyper/meta.yml
@@ -3,6 +3,7 @@ description: Computational method for finding spa types.
 keywords:
   - fasta
   - spatype
+  - spa
 tools:
   - spatyper:
       description: Computational method for finding spa types.
diff --git a/modules/nf-core/spring/compress/meta.yml b/modules/nf-core/spring/compress/meta.yml
index f1958dc57ed..8b52160940c 100644
--- a/modules/nf-core/spring/compress/meta.yml
+++ b/modules/nf-core/spring/compress/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md"
       tool_dev_url: "https://github.com/shubhamchandak94/Spring"
       doi: "10.1093/bioinformatics/bty1015"
-      licence: "['Free for non-commercial use']"
+      licence: ["Free for non-commercial use"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml
index 8f43aa93d4d..39740c50c05 100644
--- a/modules/nf-core/spring/decompress/meta.yml
+++ b/modules/nf-core/spring/decompress/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md"
       tool_dev_url: "https://github.com/shubhamchandak94/Spring"
       doi: "10.1093/bioinformatics/bty1015"
-      licence: "['Free for non-commercial use']"
+      licence: ["Free for non-commercial use"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/srst2/srst2/meta.yml b/modules/nf-core/srst2/srst2/meta.yml
index ff6f3413ee1..5d5a6876a6e 100644
--- a/modules/nf-core/srst2/srst2/meta.yml
+++ b/modules/nf-core/srst2/srst2/meta.yml
@@ -17,7 +17,7 @@ tools:
       licence: ["BSD"]
 input:
   - meta:
-      type: map0.2.0-4
+      type: map
       description: |
         Groovy Map containing sample information
         id: should be the identification number or sample name
diff --git a/modules/nf-core/stadeniolib/scramble/meta.yml b/modules/nf-core/stadeniolib/scramble/meta.yml
index 3c9d8fba6d7..8e3d6f270d8 100644
--- a/modules/nf-core/stadeniolib/scramble/meta.yml
+++ b/modules/nf-core/stadeniolib/scramble/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/jkbonfield/io_lib"
       documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
       tool_dev_url: "https://github.com/jkbonfield/io_lib"
-      licence: "['BSD']"
+      licence: ["BSD"]
 input:
   - meta:
       type: map
@@ -49,7 +49,7 @@ output:
       description: Converted reads
       pattern: "*.{sam, bam, cram}"
   - gzi:
-      type: Optional file
+      type: file
       description: gzip index file for BAM outputs
       pattern: ".{bam.gzi}"
 authors:
diff --git a/modules/nf-core/stecfinder/meta.yml b/modules/nf-core/stecfinder/meta.yml
index 93e30b86bdd..a4efed3190d 100644
--- a/modules/nf-core/stecfinder/meta.yml
+++ b/modules/nf-core/stecfinder/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/LanLab/STECFinder"
       tool_dev_url: "https://github.com/LanLab/STECFinder"
       doi: "10.3389/fcimb.2021.772574"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/stitch/meta.yml b/modules/nf-core/stitch/meta.yml
index a36d61cd896..2596fa37928 100644
--- a/modules/nf-core/stitch/meta.yml
+++ b/modules/nf-core/stitch/meta.yml
@@ -17,7 +17,7 @@ tools:
       documentation: "https://github.com/rwdavies/stitch"
       tool_dev_url: "https://github.com/rwdavies/stitch"
       doi: "10.1038/ng.3594"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/survivor/filter/meta.yml b/modules/nf-core/survivor/filter/meta.yml
index 4cb29051c3a..64565408d30 100644
--- a/modules/nf-core/survivor/filter/meta.yml
+++ b/modules/nf-core/survivor/filter/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/fritzsedlazeck/SURVIVOR/wiki"
       tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR"
       doi: "10.1038/NCOMMS14061"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/survivor/merge/meta.yml b/modules/nf-core/survivor/merge/meta.yml
index a7c2e2b3b98..57f9dd08679 100644
--- a/modules/nf-core/survivor/merge/meta.yml
+++ b/modules/nf-core/survivor/merge/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/fritzsedlazeck/SURVIVOR/wiki"
       tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR"
       doi: "10.1038/NCOMMS14061"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -20,7 +20,7 @@ input:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - vcfs:
-      type: files
+      type: file
       description: |
         The VCF files to be merged
         Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158
diff --git a/modules/nf-core/survivor/simsv/meta.yml b/modules/nf-core/survivor/simsv/meta.yml
index 88caacadee8..80b6d1c918a 100644
--- a/modules/nf-core/survivor/simsv/meta.yml
+++ b/modules/nf-core/survivor/simsv/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/fritzsedlazeck/SURVIVOR/wiki"
       tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR"
       doi: "10.1038/NCOMMS14061"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svaba/meta.yml b/modules/nf-core/svaba/meta.yml
index af04fe1a2f2..d78ea0e8c99 100644
--- a/modules/nf-core/svaba/meta.yml
+++ b/modules/nf-core/svaba/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880247/"
       tool_dev_url: "https://github.com/walaj/svaba"
       doi: "10.1101/gr.221028.117"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svanalyzer/svbenchmark/meta.yml b/modules/nf-core/svanalyzer/svbenchmark/meta.yml
index 08b2048e93d..b574cc2f3ec 100644
--- a/modules/nf-core/svanalyzer/svbenchmark/meta.yml
+++ b/modules/nf-core/svanalyzer/svbenchmark/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://svanalyzer.readthedocs.io/en/latest/index.html"
       documentation: "https://svanalyzer.readthedocs.io/en/latest/index.html"
       tool_dev_url: "https://github.com/nhansen/SVanalyzer"
-      license: "['CC0']"
+      license: ["CC0"]
 
 input:
   - meta:
diff --git a/modules/nf-core/svtk/baftest/meta.yml b/modules/nf-core/svtk/baftest/meta.yml
index 920c0af36ce..fcae45bd8dd 100644
--- a/modules/nf-core/svtk/baftest/meta.yml
+++ b/modules/nf-core/svtk/baftest/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svtk/countsvtypes/meta.yml b/modules/nf-core/svtk/countsvtypes/meta.yml
index 7952bc02597..bc398ec1e72 100644
--- a/modules/nf-core/svtk/countsvtypes/meta.yml
+++ b/modules/nf-core/svtk/countsvtypes/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       doi: "10.1038/s41586-020-2287-8"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svtk/rdtest2vcf/meta.yml b/modules/nf-core/svtk/rdtest2vcf/meta.yml
index c89ac97a1c6..c1851f5738d 100644
--- a/modules/nf-core/svtk/rdtest2vcf/meta.yml
+++ b/modules/nf-core/svtk/rdtest2vcf/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       doi: "10.1038/s41586-020-2287-8"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svtk/standardize/meta.yml b/modules/nf-core/svtk/standardize/meta.yml
index f0581cd29a8..e0d35cf4dde 100644
--- a/modules/nf-core/svtk/standardize/meta.yml
+++ b/modules/nf-core/svtk/standardize/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - args:
       type: map
diff --git a/modules/nf-core/svtk/vcf2bed/meta.yml b/modules/nf-core/svtk/vcf2bed/meta.yml
index 768b9b7c755..4b1d2e63e13 100644
--- a/modules/nf-core/svtk/vcf2bed/meta.yml
+++ b/modules/nf-core/svtk/vcf2bed/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
       tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/svtyper/svtyper/meta.yml b/modules/nf-core/svtyper/svtyper/meta.yml
index a23ceff2c14..2184620d36b 100644
--- a/modules/nf-core/svtyper/svtyper/meta.yml
+++ b/modules/nf-core/svtyper/svtyper/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/hall-lab/svtyper"
       tool_dev_url: "https://github.com/hall-lab/svtyper"
       doi: "10.1038/nmeth.3505"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/tailfindr/meta.yml b/modules/nf-core/tailfindr/meta.yml
index 240fdaa28ea..47cc2a37020 100644
--- a/modules/nf-core/tailfindr/meta.yml
+++ b/modules/nf-core/tailfindr/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/adnaniazi/tailfindr/blob/master/README.md"
       tool_dev_url: "https://github.com/adnaniazi/tailfindr"
       doi: "10.1261/rna.071332.119"
-      licence: "['AGPL v3']"
+      licence: ["AGPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/taxpasta/merge/meta.yml b/modules/nf-core/taxpasta/merge/meta.yml
index 6945d105389..d15bd049da1 100644
--- a/modules/nf-core/taxpasta/merge/meta.yml
+++ b/modules/nf-core/taxpasta/merge/meta.yml
@@ -14,7 +14,7 @@ tools:
       homepage: "https://taxpasta.readthedocs.io/"
       documentation: "https://taxpasta.readthedocs.io/"
       tool_dev_url: "https://github.com/taxprofiler/taxpasta"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/taxpasta/standardise/meta.yml b/modules/nf-core/taxpasta/standardise/meta.yml
index a902b00e02a..a4c023266d0 100644
--- a/modules/nf-core/taxpasta/standardise/meta.yml
+++ b/modules/nf-core/taxpasta/standardise/meta.yml
@@ -14,7 +14,7 @@ tools:
       homepage: "https://taxpasta.readthedocs.io/"
       documentation: "https://taxpasta.readthedocs.io/"
       tool_dev_url: "https://github.com/taxprofiler/taxpasta"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/tiara/tiara/meta.yml b/modules/nf-core/tiara/tiara/meta.yml
index 5e532c0eca1..e9d6b0553d7 100644
--- a/modules/nf-core/tiara/tiara/meta.yml
+++ b/modules/nf-core/tiara/tiara/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: https://ibe-uw.github.io/tiara/"
       tool_dev_url: "https://github.com/ibe-uw/tiara"
       doi: "10.1093/bioinformatics/btab672"
-      licence: "MIT"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/topas/gencons/meta.yml b/modules/nf-core/topas/gencons/meta.yml
index 5e7c8770c1a..4bef8632826 100644
--- a/modules/nf-core/topas/gencons/meta.yml
+++ b/modules/nf-core/topas/gencons/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/subwaystation/TOPAS/wiki/Overview-Modules"
       tool_dev_url: "https://github.com/subwaystation/TOPAS"
       doi: "10.1038/s41598-017-17723-1"
-      licence: "['CC-BY']"
+      licence: ["CC-BY"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml
index ea2c9b8eca0..8736eb12d6a 100644
--- a/modules/nf-core/transdecoder/predict/meta.yml
+++ b/modules/nf-core/transdecoder/predict/meta.yml
@@ -3,6 +3,7 @@ description: TransDecoder identifies candidate coding regions within transcript
 keywords:
   - eukaryotes
   - gff
+  - coding regions
 tools:
   - transdecoder:
       description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
@@ -35,19 +36,19 @@ output:
       description: File containing software versions
       pattern: "versions.yml"
   - pep:
-      type: amino acids fasta file
+      type: file
       description: All ORFs meeting the minimum length criteria, regardless of coding potential
       pattern: "*.{pep}"
   - gff3:
-      type: gff3 file
+      type: file
       description: Positions of all ORFs as found in the target transcripts
       pattern: "*.{gff3}"
   - cds:
-      type: nucleotide fasta file
+      type: file
       description: the nucleotide coding sequence for all detected ORFs
       pattern: "*{cds}"
   - bed:
-      type: bed file
+      type: file
       description: bed file
       pattern: "*{bed}"
 authors:
diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml
index 0486e9f5756..5c8a2fafc42 100644
--- a/modules/nf-core/trimmomatic/meta.yml
+++ b/modules/nf-core/trimmomatic/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
       documentation: "https://github.com/usadellab/Trimmomatic"
       doi: "10.1093/bioinformatics/btu170"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/truvari/bench/meta.yml b/modules/nf-core/truvari/bench/meta.yml
index 78f9abff8f8..1d8cf5bb237 100644
--- a/modules/nf-core/truvari/bench/meta.yml
+++ b/modules/nf-core/truvari/bench/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/acenglish/truvari/wiki"
       tool_dev_url: "https://github.com/ACEnglish/truvari"
       doi: "10.1186/s13059-022-02840-6"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ultra/align/meta.yml b/modules/nf-core/ultra/align/meta.yml
index 264e9ab8988..79b9e30aadb 100644
--- a/modules/nf-core/ultra/align/meta.yml
+++ b/modules/nf-core/ultra/align/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/ksahlin/uLTRA"
       tool_dev_url: "https://github.com/ksahlin/uLTRA"
       doi: "10.1093/bioinformatics/btab540"
-      licence: "['GNU GPLV3']"
+      licence: ["GNU GPLV3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml
index 3c0eda98771..1bf59abab07 100644
--- a/modules/nf-core/ultra/index/meta.yml
+++ b/modules/nf-core/ultra/index/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://github.com/ksahlin/uLTRA"
       tool_dev_url: "https://github.com/ksahlin/uLTRA"
       doi: "10.1093/bioinformatics/btab540"
-      licence: "['GNU GPLV3']"
+      licence: ["GNU GPLV3"]
 input:
   - fasta:
       type: file
diff --git a/modules/nf-core/upd/meta.yml b/modules/nf-core/upd/meta.yml
index 7682e337b64..9375d56d4c8 100644
--- a/modules/nf-core/upd/meta.yml
+++ b/modules/nf-core/upd/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://github.com/bjhall/upd
       documentation: https://github.com/bjhall/upd
       tool_dev_url: https://github.com/bjhall/upd
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta:
diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml
index 657d153125f..5c2fc921aca 100644
--- a/modules/nf-core/vardictjava/meta.yml
+++ b/modules/nf-core/vardictjava/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
       tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
       doi: "10.1093/nar/gkw227 "
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/varlociraptor/callvariants/meta.yml b/modules/nf-core/varlociraptor/callvariants/meta.yml
index 5845db58ff9..85ef816d34f 100644
--- a/modules/nf-core/varlociraptor/callvariants/meta.yml
+++ b/modules/nf-core/varlociraptor/callvariants/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://varlociraptor.github.io/docs/calling/"
       tool_dev_url: "https://github.com/varlociraptor/varlociraptor"
       doi: "10.1186/s13059-020-01993-6"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml
index 0942988331f..624b0754fa3 100644
--- a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml
+++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://varlociraptor.github.io/docs/estimating/"
       tool_dev_url: "https://github.com/varlociraptor/varlociraptor"
       doi: "10.1186/s13059-020-01993-6"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/varlociraptor/preprocess/meta.yml b/modules/nf-core/varlociraptor/preprocess/meta.yml
index 00a6227d271..7fd3de5bb8f 100644
--- a/modules/nf-core/varlociraptor/preprocess/meta.yml
+++ b/modules/nf-core/varlociraptor/preprocess/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://varlociraptor.github.io/docs/calling/"
       tool_dev_url: "https://github.com/varlociraptor/varlociraptor"
       doi: "10.1186/s13059-020-01993-6"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml
index 17f9c38db74..b091f2b1015 100644
--- a/modules/nf-core/vcf2maf/meta.yml
+++ b/modules/nf-core/vcf2maf/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/mskcc/vcf2maf"
       tool_dev_url: "https://github.com/mskcc/vcf2maf"
       doi: "10.5281/zenodo.593251"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml
index 9ce47211c37..8dc136dffdf 100644
--- a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml
+++ b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml
@@ -2,14 +2,16 @@ name: "vcflib_vcfbreakmulti"
 description: If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields
 keywords:
   - vcflib
-  - vcflib/vcfbreakmulti
+  - vcfbreakmulti
+  - multiple alleles
+  - INFO fields
 tools:
   - "vcflib":
       description: "Command-line tools for manipulating VCF files"
       homepage: https://github.com/vcflib/vcflib
       documentation: https://github.com/vcflib/vcflib#USAGE
       doi: "10.1101/2021.05.21.445151"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vcflib/vcffilter/meta.yml b/modules/nf-core/vcflib/vcffilter/meta.yml
index a6ac598d96f..f9fe81b52c0 100644
--- a/modules/nf-core/vcflib/vcffilter/meta.yml
+++ b/modules/nf-core/vcflib/vcffilter/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/vcflib/vcflib"
       tool_dev_url: "https://github.com/vcflib/vcflib"
       doi: "10.1371/journal.pcbi.1009123"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/verifybamid/verifybamid/meta.yml b/modules/nf-core/verifybamid/verifybamid/meta.yml
index 34909146a01..fa5a0252582 100644
--- a/modules/nf-core/verifybamid/verifybamid/meta.yml
+++ b/modules/nf-core/verifybamid/verifybamid/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "http://genome.sph.umich.edu/wiki/VerifyBamID"
       tool_dev_url: "https://github.com/statgen/verifyBamID"
       doi: "10.1016/j.ajhg.2012.09.004"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml
index 91f41f0d200..077f0a20c7d 100644
--- a/modules/nf-core/verifybamid/verifybamid2/meta.yml
+++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml
@@ -3,6 +3,8 @@ description: Detecting and estimating inter-sample DNA contamination became a cr
 keywords:
   - contamination
   - bam
+  - verifybamid
+  - inter-sample DNA contamination
 tools:
   - "verifybamid2":
       description: "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method."
@@ -10,7 +12,7 @@ tools:
       documentation: "http://griffan.github.io/VerifyBamID"
       tool_dev_url: "https://github.com/Griffan/VerifyBamID"
       doi: "10.1101/gr.246934.118"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml
index f9cdcd951a5..ef52cf111c5 100644
--- a/modules/nf-core/vrhyme/extractunbinned/meta.yml
+++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/AnantharamanLab/vRhyme
       tool_dev_url: https://github.com/AnantharamanLab/vRhyme
       doi: 10.1093/nar/gkac341
-      licence: "['GPL v3 license', 'GPL v3']"
+      licence: ["GPL v3 license", "GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml
index a2076618c00..df8aea7c9bb 100644
--- a/modules/nf-core/vrhyme/linkbins/meta.yml
+++ b/modules/nf-core/vrhyme/linkbins/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/AnantharamanLab/vRhyme
       tool_dev_url: https://github.com/AnantharamanLab/vRhyme
       doi: 10.1093/nar/gkac341
-      licence: "['GPL v3 license', 'GPL v3']"
+      licence: ["GPL v3 license", "GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vrhyme/vrhyme/meta.yml b/modules/nf-core/vrhyme/vrhyme/meta.yml
index c011b3a4b66..659d805b88c 100644
--- a/modules/nf-core/vrhyme/vrhyme/meta.yml
+++ b/modules/nf-core/vrhyme/vrhyme/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: https://github.com/AnantharamanLab/vRhyme
       tool_dev_url: https://github.com/AnantharamanLab/vRhyme
       doi: 10.1093/nar/gkac341
-      licence: "['GPL v3', 'GPL v3 license']"
+      licence: ["GPL v3", "GPL v3 license"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vsearch/sintax/meta.yml b/modules/nf-core/vsearch/sintax/meta.yml
index 6346260ef73..c9a29272485 100644
--- a/modules/nf-core/vsearch/sintax/meta.yml
+++ b/modules/nf-core/vsearch/sintax/meta.yml
@@ -3,13 +3,14 @@ description: Taxonomic classification using the sintax algorithm.
 keywords:
   - vsearch
   - sintax
+  - taxonomic classification
 tools:
   - "vsearch":
       description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)"
       homepage: "https://github.com/torognes/vsearch"
       tool_dev_url: "https://github.com/torognes/vsearch"
       doi: "10.7717/peerj.2584"
-      licence: "['GPL v3-or-later OR BSD-2-clause']"
+      licence: ["GPL v3-or-later OR BSD-2-clause"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml
index dc953946a17..ba56f1778e4 100644
--- a/modules/nf-core/vsearch/usearchglobal/meta.yml
+++ b/modules/nf-core/vsearch/usearchglobal/meta.yml
@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/torognes/vsearch"
       tool_dev_url: "https://github.com/torognes/vsearch"
       doi: "10.7717/peerj.2584"
-      licence: "['GPL v3-or-later OR BSD-2-clause']"
+      licence: ["GPL v3-or-later OR BSD-2-clause"]
 input:
   - meta:
       type: map
@@ -25,7 +25,7 @@ input:
       description: Reference database file in FASTA or UDB format
       pattern: "*"
   - idcutoff:
-      type: real
+      type: float
       description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)
   - outoption:
       type: string
diff --git a/modules/nf-core/vt/decompose/meta.yml b/modules/nf-core/vt/decompose/meta.yml
index 8b9decd8288..0a08d876730 100644
--- a/modules/nf-core/vt/decompose/meta.yml
+++ b/modules/nf-core/vt/decompose/meta.yml
@@ -13,7 +13,7 @@ tools:
       homepage: "https://genome.sph.umich.edu/wiki/Vt"
       documentation: "https://genome.sph.umich.edu/wiki/Vt"
       tool_dev_url: "https://github.com/atks/vt"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/vt/normalize/meta.yml b/modules/nf-core/vt/normalize/meta.yml
index af46bf63c1d..37e7bca1612 100644
--- a/modules/nf-core/vt/normalize/meta.yml
+++ b/modules/nf-core/vt/normalize/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://genome.sph.umich.edu/wiki/Vt"
       documentation: "https://genome.sph.umich.edu/wiki/Vt"
       tool_dev_url: "https://github.com/atks/vt"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/wgsim/meta.yml b/modules/nf-core/wgsim/meta.yml
index 89e041b406f..b57c67b8d18 100644
--- a/modules/nf-core/wgsim/meta.yml
+++ b/modules/nf-core/wgsim/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/lh3/wgsim"
       documentation: "https://github.com/lh3/wgsim"
       tool_dev_url: "https://github.com/lh3/wgsim"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/whamg/meta.yml b/modules/nf-core/whamg/meta.yml
index 62f4cc566df..fc19fce9b89 100644
--- a/modules/nf-core/whamg/meta.yml
+++ b/modules/nf-core/whamg/meta.yml
@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/zeeev/wham"
       tool_dev_url: "https://github.com/zeeev/wham"
       doi: "10.1371/journal.pcbi.1004572"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/wisecondorx/convert/meta.yml b/modules/nf-core/wisecondorx/convert/meta.yml
index b6d0b457460..d70d9d69ab2 100644
--- a/modules/nf-core/wisecondorx/convert/meta.yml
+++ b/modules/nf-core/wisecondorx/convert/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/wisecondorx/gender/meta.yml b/modules/nf-core/wisecondorx/gender/meta.yml
index 0ffd2bea4cf..cd4da24f7bc 100644
--- a/modules/nf-core/wisecondorx/gender/meta.yml
+++ b/modules/nf-core/wisecondorx/gender/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/wisecondorx/newref/meta.yml b/modules/nf-core/wisecondorx/newref/meta.yml
index 8229904596b..d5efefeb53f 100644
--- a/modules/nf-core/wisecondorx/newref/meta.yml
+++ b/modules/nf-core/wisecondorx/newref/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/wisecondorx/predict/meta.yml b/modules/nf-core/wisecondorx/predict/meta.yml
index bb2313e0dba..849f1a98436 100644
--- a/modules/nf-core/wisecondorx/predict/meta.yml
+++ b/modules/nf-core/wisecondorx/predict/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
-      licence: "['Attribution-NonCommercial-ShareAlike CC BY-NC-SA']"
+      licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml
index 8798ae17cd7..7ddcc7781ee 100644
--- a/modules/nf-core/yahs/meta.yml
+++ b/modules/nf-core/yahs/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/c-zhou/yahs"
       tool_dev_url: "https://github.com/c-zhou/yahs"
       doi: "10.1093/bioinformatics/btac808"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   # Only when we have meta
   - meta: