diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index e1e1f4bc57d..b45e04d467a 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -1,18 +1,22 @@
 name: "nf-test Action"
 description: "Runs nf-test with common setup steps"
 inputs:
-  path:
-    description: "Path to test"
-    required: true
   profile:
     description: "Profile to use"
     required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  tags:
+    description: "Tags to test (`<tags>[,<tags>...]`)"
+    required: false
 
 runs:
   using: "composite"
   steps:
-    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
     - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
       with:
         distribution: "temurin"
@@ -20,6 +24,8 @@ runs:
 
     - name: Setup Nextflow
       uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
       uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
@@ -29,7 +35,7 @@ runs:
     - name: Install nf-test
       uses: nf-core/setup-nf-test@v1
       with:
-        version: "0.9.2"
+        version: "${{ env.NFTEST_VERSION }}"
         install-pdiff: true
 
     - name: Setup apptainer
@@ -56,20 +62,31 @@ runs:
       if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
       shell: bash
       run: |
+        python -m pip install cryptography
         nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
 
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
         SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
         SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        TAGS: ${{ inputs.tags && format('--tag {0}', inputs.tags) || '' }}
+        NFT_WORKDIR: "~"
       run: |
-        NFT_WORKDIR=~ \
         nf-test test \
           --profile=${{ inputs.profile }} \
           --tap=test.tap \
           --verbose \
-          ${{ inputs.path }}
+          --ci \
+          --changed-since HEAD^ \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
+          --filter process,workflow \
+          --follow-dependencies \
+          ${{ env.TAGS }}
+
+      # TODO If no test.tap, then make one to spoof?
     - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
       if: ${{ inputs.path != '' }}
       with:
diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
new file mode 100644
index 00000000000..2ef7216da3e
--- /dev/null
+++ b/.github/conda_skip.yml
@@ -0,0 +1,184 @@
+# TODO What do we do with these?
+# I think we can require Docker,modules,Shard 1..Singularity,subworkflows,3 and skip the condas now
+exclude:
+  - path: modules/nf-core/nf-test
+  - profile: conda
+    path: modules/nf-core/angsd/gl
+  - profile: conda
+    path: modules/nf-core/annotsv/installannotations
+  - profile: conda
+    path: modules/nf-core/happy/sompy
+  - profile: conda
+    path: modules/nf-core/backsub
+  - profile: conda
+    path: modules/nf-core/bakta/bakta
+  - profile: conda
+    path: modules/nf-core/bakta/baktadbdownload
+  - profile: conda
+    path: modules/nf-core/bases2fastq
+  - profile: conda
+    path: modules/nf-core/bcl2fastq
+  - profile: conda
+    path: modules/nf-core/bclconvert
+  - profile: conda
+    path: modules/nf-core/celesta
+  - profile: conda
+    path: modules/nf-core/cellpose
+  - profile: conda
+    path: modules/nf-core/cellranger/count
+  - profile: conda
+    path: modules/nf-core/cellranger/mkfastq
+  - profile: conda
+    path: modules/nf-core/cellranger/mkgtf
+  - profile: conda
+    path: modules/nf-core/cellranger/mkref
+  - profile: conda
+    path: modules/nf-core/cellranger/mkvdjref
+  - profile: conda
+    path: modules/nf-core/cellranger/multi
+  - profile: conda
+    path: modules/nf-core/cellranger/vdj
+  - profile: conda
+    path: modules/nf-core/checkqc
+  - profile: conda
+    path: modules/nf-core/custom/dumpsoftwareversions
+  - profile: conda
+    path: modules/nf-core/deepcell/mesmer
+  - profile: conda
+    path: modules/nf-core/deepsomatic
+  - profile: singularity
+    path: modules/nf-core/deepsomatic
+  - profile: conda
+    path: modules/nf-core/deepvariant
+  - profile: conda
+    path: modules/nf-core/deepvariant/callvariants
+  - profile: conda
+    path: modules/nf-core/deepvariant/makeexamples
+  - profile: conda
+    path: modules/nf-core/deepvariant/postprocessvariants
+  - profile: conda
+    path: modules/nf-core/deepvariant/rundeepvariant
+  - profile: conda
+    path: modules/nf-core/deepvariant/vcfstatsreport
+  - profile: conda
+    path: modules/nf-core/doubletdetection
+  - profile: conda
+    path: modules/nf-core/ensemblvep/vep
+  - profile: conda
+    path: modules/nf-core/fastk/fastk
+  - profile: conda
+    path: modules/nf-core/cellrangerarc/mkgtf
+  - profile: conda
+    path: modules/nf-core/fastk/histex
+  - profile: conda
+    path: modules/nf-core/fastk/merge
+  - profile: conda
+    path: modules/nf-core/fcs/fcsadaptor
+  - profile: conda
+    path: modules/nf-core/fcs/fcsgx
+  - profile: conda
+    path: modules/nf-core/ganon/buildcustom
+  - profile: conda
+    path: modules/nf-core/ganon/classify
+  - profile: conda
+    path: modules/nf-core/ganon/report
+  - profile: conda
+    path: modules/nf-core/ganon/table
+  - profile: conda
+    path: modules/nf-core/gatk4/cnnscorevariants
+  - profile: conda
+    path: modules/nf-core/gatk4/determinegermlinecontigploidy
+  - profile: conda
+    path: modules/nf-core/genescopefk
+  - profile: conda
+    path: modules/nf-core/ilastik/multicut
+  - profile: conda
+    path: modules/nf-core/ilastik/pixelclassification
+  - profile: conda
+    path: modules/nf-core/imputeme/vcftoprs
+  - profile: conda
+    path: modules/nf-core/mcstaging/imc2mc
+  - profile: conda
+    path: modules/nf-core/mcquant
+  - profile: conda
+    path: modules/nf-core/mcstaging/phenoimager2mc
+  - profile: conda
+    path: modules/nf-core/merquryfk/katcomp
+  - profile: conda
+    path: modules/nf-core/merquryfk/katgc
+  - profile: conda
+    path: modules/nf-core/merquryfk/merquryfk
+  - profile: conda
+    path: modules/nf-core/merquryfk/ploidyplot
+  - profile: conda
+    path: modules/nf-core/molkartgarage/clahe
+  - profile: conda
+    path: modules/nf-core/quartonotebook
+  - profile: conda
+    path: modules/nf-core/scimap/spatiallda
+  - profile: conda
+    path: modules/nf-core/sentieon/bwaindex
+  - profile: conda
+    path: modules/nf-core/sentieon/bwamem
+  - profile: conda
+    path: modules/nf-core/sentieon/datametrics
+  - profile: conda
+    path: modules/nf-core/sentieon/dedup
+  - profile: conda
+    path: modules/nf-core/sentieon/qualcal
+  - profile: conda
+    path: modules/nf-core/spaceranger/mkgtf
+  - profile: conda
+    path: modules/nf-core/spaceranger/mkref
+  - profile: conda
+    path: modules/nf-core/spaceranger/count
+  - profile: conda
+    path: modules/nf-core/spotiflow
+  - profile: conda
+    path: modules/nf-core/svanalyzer/svbenchmark
+  - profile: conda
+    path: modules/nf-core/universc
+  - profile: singularity
+    path: modules/nf-core/universc
+  - profile: conda
+    path: modules/nf-core/vt/decompose
+  - profile: singularity
+    path: modules/nf-core/bases2fastq
+  - profile: conda
+    path: modules/nf-core/wittyer
+  - profile: conda
+    path: modules/nf-core/islandpath
+  - profile: conda
+    path: modules/nf-core/scimap/mcmicro
+  - profile: conda
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: docker_self_hosted
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: singularity
+    path: modules/nf-core/parabricks/fq2bammeth
+  - profile: conda
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: docker_self_hosted
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: singularity
+    path: modules/nf-core/parabricks/fq2bam
+  - profile: conda
+    path: subworkflows/nf-core/vcf_annotate_ensemblvep
+  - profile: conda
+    path: subworkflows/nf-core/bcl_demultiplex
+  - profile: conda
+    path: subworkflows/nf-core/deepvariant
+  - profile: conda
+    path: subworkflows/nf-core/fastq_align_bamcmp_bwa
+  - profile: conda
+    path: subworkflows/nf-core/fastq_align_bwa
+  - profile: conda
+    path: subworkflows/nf-core/fasta_newick_epang_gappa
+  - profile: conda
+    path: modules/nf-core/xeniumranger/relabel
+  - profile: conda
+    path: modules/nf-core/xeniumranger/rename
+  - profile: conda
+    path: modules/nf-core/xeniumranger/resegment
+  - profile: conda
+    path: modules/nf-core/xeniumranger/import-segmentation
diff --git a/.github/renovate.json5 b/.github/renovate.json5
index 46af7821e36..eacaed1524b 100644
--- a/.github/renovate.json5
+++ b/.github/renovate.json5
@@ -7,8 +7,24 @@
     "prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
     "packageRules": [
         {
-            "matchDatasources": ["conda", "pypi", "docker"],
+            "matchDatasources": [
+                "conda",
+                "pypi",
+                "docker"
+            ],
             "automerge": false
         }
-    ]
+    ],
+        "customManagers": [
+            {
+                "customType": "regex",
+                "fileMatch": [
+                    "(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$",
+                    "(^|/)action\\.ya?ml$"
+                ],
+                "matchStrings": [
+                    "# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
+                ]
+            }
+        ]
 }
diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
new file mode 100644
index 00000000000..92188ed9702
--- /dev/null
+++ b/.github/workflows/gpu-tests.yml
@@ -0,0 +1,73 @@
+name: Run GPU nf-tests
+on:
+  push:
+    branches:
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
+  pull_request:
+    branches: [master]
+    paths:
+      - ".github/workflows/gpu-tests.yml"
+      - "modules/nf-core/parabricks/**"
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "self-hosted"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.2"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
+
+jobs:
+  nf-test-gpu:
+    runs-on: "gpu"
+    name: "GPU | ${{ matrix.tags}} | ${{ matrix.profile }} | ${{ matrix.shard }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: [1, 2]
+        profile: [docker_self_hosted, singularity] # conda?
+        # TODO Pass these in from GitHub PR trigger events
+        tags:
+          - parabricks/applybqsr
+          - parabricks/fq2bam
+          - parabricks/fq2bammeth
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: 2
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+      - name: Run nf-test Action
+        uses: ./.github/actions/nf-test-action
+        env:
+          SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
+          SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
+          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
+          SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        with:
+          profile: ${{ matrix.profile }},gpu
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+          tags: ${{matrix.tags}},gpu
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000000..756894a27b0
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,170 @@
+name: Run Linting
+on:
+  push:
+    branches:
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "self-hosted"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VER: "24.10.1"
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
+        with:
+          extra_args: ""
+
+  ###################
+  # nf-core linting #
+  ###################
+  # TODO Move these to pre-commit
+  # https://github.com/nf-core/tools/pull/3141
+  nf-core-changes:
+    name: nf-core-changes
+    runs-on: ubuntu-latest
+    outputs:
+      tags: ${{ steps.filter.outputs.changes }}
+      modules: ${{ steps.tags.outputs.modules }}
+      subworkflows: ${{ steps.tags.outputs.subworkflows }}
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
+
+      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+          token: ""
+
+      - name: Fetch module tags
+        id: tags
+        run: |
+          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
+
+      - name: debug
+        run: |
+          echo ${{ steps.tags.outputs.modules }}
+          echo ${{ steps.tags.outputs.subworkflows }}
+
+  nf-core-lint-modules:
+    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
+    name: nf-core lint modules
+    needs: nf-core-changes
+    if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }}
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}"
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: |
+            ${{ runner.os }}-pip
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+
+  nf-core-lint-subworkflows:
+    runs-on: ubuntu-latest
+    name: nf-core lint subworkflows
+    needs: nf-core-changes
+    if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }}
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}"
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core subworkflows lint ${{ matrix.tags }}
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [nf-core-lint-modules, nf-core-lint-subworkflows]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 00000000000..6eb3525404a
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,73 @@
+name: Run nf-test
+on:
+  push:
+    branches:
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "self-hosted"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.2"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
+
+jobs:
+  nf-test:
+    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
+    # NOTE I think this is the cleanest way to get them organized
+    # process | conda | 1
+    # process | conda | 2
+    # process | conda | 3
+    # process | docker_self_hosted | 1
+    # ...
+    # workflow | singularity | 3
+    name: "${{ matrix.profile }} | ${{ matrix.shard }}"
+    # TODO
+    # needs: get-number-of-shards
+    # if: ${{ fromJSON(needs.get-number-of-shards.outputs.shards) != fromJSON('["1", "0"]') }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # NOTE We could split these, but there's probably going to be more process tests than workflow tests, so we're just going to combine them all and bump up the shards for now
+        # NOTE The name of the test would be name: "${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}"
+        # filter: [process, workflow]
+        profile: [conda, docker_self_hosted, singularity]
+        shard: [1, 2, 3, 4, 5]
+    env:
+      # FIXME Bumping them up to make the transition smooth, then we can throttle them back
+      TOTAL_SHARDS: 5
+      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
+      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+      - name: Run nf-test Action
+        uses: ./.github/actions/nf-test-action
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
new file mode 100644
index 00000000000..4d4a96d0f38
--- /dev/null
+++ b/.github/workflows/pytest-workflow.yml
@@ -0,0 +1,346 @@
+name: Run pytest-workflow
+on:
+  push:
+    branches:
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "self-hosted"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
+
+jobs:
+  pytest-changes:
+    name: pytest-changes
+    runs-on: ubuntu-latest
+    outputs:
+      tags: ${{ steps.filter.outputs.changes }}
+      modules: ${{ steps.tags.outputs.modules }}
+      subworkflows: ${{ steps.tags.outputs.subworkflows }}
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          fetch-depth: 2 # To retrieve the preceding commit.
+
+      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+          token: ""
+
+      - name: Fetch module tags
+        id: tags
+        run: |
+          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
+          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
+
+      - name: debug
+        run: |
+          echo ${{ steps.tags.outputs.modules }}
+          echo ${{ steps.tags.outputs.subworkflows }}
+
+  pytest:
+    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
+    name: pytest
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.tags != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
+        profile: [conda, docker, singularity]
+        exclude:
+          - tags: nf-test
+          - profile: conda
+            tags: backsub
+          - profile: conda
+            tags: bases2fastq
+          - profile: singularity
+            tags: bases2fastq
+          - profile: conda
+            tags: basicpy
+          - profile: conda
+            tags: bcl2fastq
+          - profile: conda
+            tags: bclconvert
+          - profile: conda
+            tags: bwa/aln
+          - profile: conda
+            tags: bwa/index
+          - profile: conda
+            tags: bwa/mem
+          - profile: conda
+            tags: bwa/sampe
+          - profile: conda
+            tags: bwa/samse
+          - profile: conda
+            tags: cellpose
+          - profile: conda
+            tags: cellrangerarc/count
+          - profile: conda
+            tags: cellrangerarc/mkfastq
+          - profile: conda
+            tags: cellrangerarc/mkref
+          - profile: conda
+            tags: cellrangeratac/count
+          - profile: conda
+            tags: cellrangeratac/mkfastq
+          - profile: conda
+            tags: cellrangeratac/mkref
+          - profile: conda
+            tags: checkm2/databasedownload
+          - profile: conda
+            tags: checkm2/predict
+          - profile: conda
+            tags: controlfreec/makegraph2
+          - profile: conda
+            tags: coreograph
+          - profile: conda
+            tags: deepcell/mesmer
+          - profile: conda
+            tags: deepvariant
+          - profile: conda
+            tags: fastani
+          - profile: conda
+            tags: fastk/fastk
+          - profile: conda
+            tags: fastk/histex
+          - profile: conda
+            tags: fastk/merge
+          - profile: conda
+            tags: fcs/fcsadaptor
+          - profile: conda
+            tags: fcs/fcsgx
+          - profile: conda
+            tags: gatk4/cnnscorevariants
+          - profile: conda
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: singularity
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: conda
+            tags: gatk4/germlinecnvcaller
+          - profile: conda
+            tags: gatk4/postprocessgermlinecnvcalls
+          - profile: conda
+            tags: genescopefk
+          - profile: conda
+            tags: happy/sompy
+          - profile: conda
+            tags: hlala/preparegraph
+          - profile: conda
+            tags: ilastik/multicut
+          - profile: conda
+            tags: ilastik/pixelclassification
+          - profile: conda
+            tags: imputeme/vcftoprs
+          - profile: conda
+            tags: islandpath
+          - profile: conda
+            tags: manta/convertinversion
+          - profile: conda
+            tags: mcstaging/imc2mc
+          - profile: conda
+            tags: mcquant
+          - profile: conda
+            tags: medaka
+          - profile: conda
+            tags: merquryfk/katcomp
+          - profile: conda
+            tags: merquryfk/katgc
+          - profile: conda
+            tags: merquryfk/merquryfk
+          - profile: conda
+            tags: merquryfk/ploidyplot
+          - profile: conda
+            tags: minimap2/align
+          - profile: conda
+            tags: mitohifi/findmitoreference
+          - profile: conda
+            tags: mitohifi/mitohifi
+          - profile: conda
+            tags: nanoplot
+          - profile: conda
+            tags: ncbitools/vecscreen
+          - profile: conda
+            tags: parabricks/applybqsr
+          - profile: conda
+            tags: parabricks/dbsnp
+          - profile: conda
+            tags: parabricks/deepvariant
+          - profile: conda
+            tags: parabricks/fq2bam
+          - profile: conda
+            tags: parabricks/genotypegvcf
+          - profile: conda
+            tags: parabricks/haplotypecaller
+          - profile: conda
+            tags: parabricks/indexgvcf
+          - profile: conda
+            tags: parabricks/mutectcaller
+          - profile: conda
+            tags: picard/collecthsmetrics
+          - profile: conda
+            tags: picard/collectwgsmetrics
+          - profile: conda
+            tags: sentieon/applyvarcal
+          - profile: conda
+            tags: sentieon/datametrics
+          - profile: conda
+            tags: sentieon/dnamodelapply
+          - profile: conda
+            tags: sentieon/dnascope
+          - profile: conda
+            tags: sentieon/readwriter
+          - profile: conda
+            tags: sentieon/tnfilter
+          - profile: conda
+            tags: sentieon/tnhaplotyper2
+          - profile: conda
+            tags: sentieon/tnscope
+          - profile: conda
+            tags: sentieon/varcal
+          - profile: conda
+            tags: sentieon/wgsmetrics
+          - profile: conda
+            tags: subworkflows/bam_qc_picard
+          - profile: conda
+            tags: subworkflows/bcl_demultiplex
+          - profile: conda
+            tags: subworkflows/fasta_clean_fcs
+          - profile: conda
+            tags: svanalyzer/svbenchmark
+          - profile: conda
+            tags: universc
+          - profile: singularity
+            tags: universc
+          - profile: conda
+            tags: vt/decompose
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+      - name: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+        id: cache-pip-pytest
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pytest
+          restore-keys: |
+            ${{ runner.os }}-pip-pytest
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography
+
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ env.NXF_VERSION }}
+
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge,bioconda
+          python-version: "3.11"
+
+      - name: Conda setup
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/ubuntu/pytest_workflow_*/*/.nextflow.log
+            /home/ubuntu/pytest_workflow_*/*/log.out
+            /home/ubuntu/pytest_workflow_*/*/log.err
+            /home/ubuntu/pytest_workflow_*/*/work
+            !/home/ubuntu/pytest_workflow_*/*/work/conda
+            !/home/ubuntu/pytest_workflow_*/*/work/singularity
+            !${{ github.workspace }}/.singularity
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [pytest-changes, pytest]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 736b2c9eae9..00000000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,745 +0,0 @@
-name: Run tests
-on:
-  push:
-    branches:
-      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
-      - "renovate/**" # branches Renovate creates
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-  workflow_dispatch:
-    inputs:
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-env:
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
-        # 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: "--all-files"
-
-  prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - name: Install NodeJS
-        uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier@3.2.5
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  editorconfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # 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)
-
-  pytest-changes:
-    name: pytest-changes
-    runs-on: ubuntu-latest
-    outputs:
-      tags: ${{ steps.filter.outputs.changes }}
-      modules: ${{ steps.tags.outputs.modules }}
-      subworkflows: ${{ steps.tags.outputs.subworkflows }}
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 2 # To retrieve the preceding commit.
-
-      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-          token: ""
-
-      - name: Fetch module tags
-        id: tags
-        run: |
-          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
-          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT
-
-      - name: debug
-        run: |
-          echo ${{ steps.tags.outputs.modules }}
-          echo ${{ steps.tags.outputs.subworkflows }}
-
-  nf-test-changes:
-    name: nf-test-changes
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose detected tags as 'modules' and 'workflows' output variables
-      paths: ${{ steps.list.outputs.components }}
-      modules: ${{ steps.outputs.outputs.modules }}
-      subworkflows: ${{ steps.outputs.outputs.subworkflows}}
-      # Prod for version bumping
-
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: List nf-test files
-        id: list
-        uses: adamrtalbot/detect-nf-test-changes@7c8be3ffd0d6538312b363c8c949dbbf5f26c3dd # v0.0.4
-        with:
-          head: ${{ github.sha }}
-          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
-          n_parents: 2
-
-      - name: Separate modules and subworkflows
-        id: outputs
-        run: |
-          echo modules=$(echo '${{ steps.list.outputs.components }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/nf-core/"; ""))') >> $GITHUB_OUTPUT
-          echo subworkflows=$(echo '${{ steps.list.outputs.components }}' | jq '. | map(select(contains("subworkflows"))) | map(gsub("subworkflows/nf-core/"; ""))') >> $GITHUB_OUTPUT
-
-      - name: debug
-        run: |
-          echo ${{ steps.filter.outputs.components }}
-          echo ${{ steps.outputs.outputs.modules }}
-          echo ${{ steps.outputs.outputs.subworkflows }}
-
-  nf-core-lint-modules:
-    runs-on: ${{ github.event.inputs.runners  || 'ubuntu-latest' }}
-    name: nf-core-lint-modules
-    needs: [pytest-changes, nf-test-changes]
-    if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }}
-    strategy:
-      fail-fast: false
-      matrix:
-        tags:
-          [
-            "${{ fromJson(needs.pytest-changes.outputs.modules) }}",
-            "${{ fromJson(needs.nf-test-changes.outputs.modules) }}",
-          ]
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
-        id: cache-pip
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip
-          restore-keys: |
-            ${{ runner.os }}-pip
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
-      - name: Lint module ${{ matrix.tags }}
-        run: nf-core modules lint ${{ matrix.tags }}
-
-  nf-core-lint-subworkflows:
-    runs-on: ubuntu-latest
-    name: nf-core-lint-modules
-    needs: [pytest-changes, nf-test-changes]
-    if: ${{ (needs.pytest-changes.outputs.subworkflows != '[]') || ( needs.nf-test-changes.outputs.subworkflows != '[]') }}
-    strategy:
-      fail-fast: false
-      matrix:
-        tags:
-          [
-            "${{ fromJson(needs.pytest-changes.outputs.subworkflows) }}",
-            "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}",
-          ]
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2
-
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
-
-      - name: Lint module ${{ matrix.tags }}
-        run: nf-core subworkflows lint ${{ matrix.tags }}
-
-  pytest:
-    runs-on: ${{ github.event.inputs.runners  || 'ubuntu-latest' }}
-    name: pytest
-    needs: [pytest-changes]
-    if: needs.pytest-changes.outputs.tags != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
-        profile: [conda, docker, singularity]
-        exclude:
-          - tags: nf-test
-          - profile: conda
-            tags: backsub
-          - profile: conda
-            tags: bases2fastq
-          - profile: singularity
-            tags: bases2fastq
-          - profile: conda
-            tags: basicpy
-          - profile: conda
-            tags: bcl2fastq
-          - profile: conda
-            tags: bclconvert
-          - profile: conda
-            tags: bwa/aln
-          - profile: conda
-            tags: bwa/index
-          - profile: conda
-            tags: bwa/mem
-          - profile: conda
-            tags: bwa/sampe
-          - profile: conda
-            tags: bwa/samse
-          - profile: conda
-            tags: cellpose
-          - profile: conda
-            tags: cellrangerarc/count
-          - profile: conda
-            tags: cellrangerarc/mkfastq
-          - profile: conda
-            tags: cellrangerarc/mkref
-          - profile: conda
-            tags: cellrangeratac/count
-          - profile: conda
-            tags: cellrangeratac/mkfastq
-          - profile: conda
-            tags: cellrangeratac/mkref
-          - profile: conda
-            tags: checkm2/databasedownload
-          - profile: conda
-            tags: checkm2/predict
-          - profile: conda
-            tags: controlfreec/makegraph2
-          - profile: conda
-            tags: coreograph
-          - profile: conda
-            tags: deepcell/mesmer
-          - profile: conda
-            tags: deepvariant
-          - profile: conda
-            tags: fastani
-          - profile: conda
-            tags: fastk/fastk
-          - profile: conda
-            tags: fastk/histex
-          - profile: conda
-            tags: fastk/merge
-          - profile: conda
-            tags: fcs/fcsadaptor
-          - profile: conda
-            tags: fcs/fcsgx
-          - profile: conda
-            tags: gatk4/cnnscorevariants
-          - profile: conda
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: singularity
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: conda
-            tags: gatk4/germlinecnvcaller
-          - profile: conda
-            tags: gatk4/postprocessgermlinecnvcalls
-          - profile: conda
-            tags: genescopefk
-          - profile: conda
-            tags: happy/sompy
-          - profile: conda
-            tags: hlala/preparegraph
-          - profile: conda
-            tags: ilastik/multicut
-          - profile: conda
-            tags: ilastik/pixelclassification
-          - profile: conda
-            tags: imputeme/vcftoprs
-          - profile: conda
-            tags: islandpath
-          - profile: conda
-            tags: manta/convertinversion
-          - profile: conda
-            tags: mcstaging/imc2mc
-          - profile: conda
-            tags: mcquant
-          - profile: conda
-            tags: medaka
-          - profile: conda
-            tags: merquryfk/katcomp
-          - profile: conda
-            tags: merquryfk/katgc
-          - profile: conda
-            tags: merquryfk/merquryfk
-          - profile: conda
-            tags: merquryfk/ploidyplot
-          - profile: conda
-            tags: minimap2/align
-          - profile: conda
-            tags: mitohifi/findmitoreference
-          - profile: conda
-            tags: mitohifi/mitohifi
-          - profile: conda
-            tags: nanoplot
-          - profile: conda
-            tags: ncbitools/vecscreen
-          - profile: conda
-            tags: parabricks/dbsnp
-          - profile: conda
-            tags: parabricks/deepvariant
-          - profile: conda
-            tags: parabricks/genotypegvcf
-          - profile: conda
-            tags: parabricks/haplotypecaller
-          - profile: conda
-            tags: parabricks/indexgvcf
-          - profile: conda
-            tags: parabricks/mutectcaller
-          - profile: conda
-            tags: picard/collecthsmetrics
-          - profile: conda
-            tags: picard/collectwgsmetrics
-          - profile: conda
-            tags: sentieon/applyvarcal
-          - profile: conda
-            tags: sentieon/datametrics
-          - profile: conda
-            tags: sentieon/dnamodelapply
-          - profile: conda
-            tags: sentieon/dnascope
-          - profile: conda
-            tags: sentieon/readwriter
-          - profile: conda
-            tags: sentieon/tnfilter
-          - profile: conda
-            tags: sentieon/tnhaplotyper2
-          - profile: conda
-            tags: sentieon/tnscope
-          - profile: conda
-            tags: sentieon/varcal
-          - profile: conda
-            tags: sentieon/wgsmetrics
-          - profile: conda
-            tags: subworkflows/bam_qc_picard
-          - profile: conda
-            tags: subworkflows/bcl_demultiplex
-          - profile: conda
-            tags: subworkflows/fasta_clean_fcs
-          - profile: conda
-            tags: svanalyzer/svbenchmark
-          - profile: conda
-            tags: universc
-          - profile: singularity
-            tags: universc
-          - profile: conda
-            tags: vt/decompose
-    env:
-      NXF_ANSI_LOG: false
-
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
-        id: cache-pip-pytest
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pytest
-          restore-keys: |
-            ${{ runner.os }}-pip-pytest
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow cryptography
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - name: Setup Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
-        with:
-          miniconda-version: "latest"
-          channels: conda-forge,bioconda
-          python-version: ${{ matrix.python-version }}
-          conda-remove-defaults: true
-
-      - name: Conda setup
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      # Test the module
-      - name: Run pytest-workflow
-        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt-get update > /dev/null
-          sudo apt-get install bat > /dev/null
-          batcat --decorations=always --color=always /home/ubuntu/pytest_workflow_*/*/log.{out,err}
-
-      - name: Setting global variables
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        id: parsed
-        with:
-          script: |
-            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
-          result-encoding: string
-
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
-        with:
-          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
-          path: |
-            /home/ubuntu/pytest_workflow_*/*/.nextflow.log
-            /home/ubuntu/pytest_workflow_*/*/log.out
-            /home/ubuntu/pytest_workflow_*/*/log.err
-            /home/ubuntu/pytest_workflow_*/*/work
-            !/home/ubuntu/pytest_workflow_*/*/work/conda
-            !/home/ubuntu/pytest_workflow_*/*/work/singularity
-            !${{ github.workspace }}/.singularity
-
-  nf-test:
-    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
-    name: nf-test
-    needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' )
-    strategy:
-      fail-fast: false
-      matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
-        profile: [conda, docker_self_hosted, singularity]
-        exclude:
-          - path: modules/nf-core/nf-test
-          - profile: conda
-            path: modules/nf-core/angsd/gl
-          - profile: conda
-            path: modules/nf-core/annotsv/installannotations
-          - profile: conda
-            path: modules/nf-core/happy/sompy
-          - profile: conda
-            path: modules/nf-core/backsub
-          - profile: conda
-            path: modules/nf-core/bakta/bakta
-          - profile: conda
-            path: modules/nf-core/bakta/baktadbdownload
-          - profile: conda
-            path: modules/nf-core/bases2fastq
-          - profile: conda
-            path: modules/nf-core/bcl2fastq
-          - profile: conda
-            path: modules/nf-core/bclconvert
-          - profile: conda
-            path: modules/nf-core/celesta
-          - profile: conda
-            path: modules/nf-core/cellpose
-          - profile: conda
-            path: modules/nf-core/cellranger/count
-          - profile: conda
-            path: modules/nf-core/cellranger/mkfastq
-          - profile: conda
-            path: modules/nf-core/cellranger/mkgtf
-          - profile: conda
-            path: modules/nf-core/cellranger/mkref
-          - profile: conda
-            path: modules/nf-core/cellranger/mkvdjref
-          - profile: conda
-            path: modules/nf-core/cellranger/multi
-          - profile: conda
-            path: modules/nf-core/cellranger/vdj
-          - profile: conda
-            path: modules/nf-core/checkqc
-          - profile: conda
-            path: modules/nf-core/custom/dumpsoftwareversions
-          - profile: conda
-            path: modules/nf-core/deepcell/mesmer
-          - profile: conda
-            path: modules/nf-core/deepsomatic
-          - profile: singularity
-            path: modules/nf-core/deepsomatic
-          - profile: conda
-            path: modules/nf-core/deepvariant
-          - profile: conda
-            path: modules/nf-core/deepvariant/callvariants
-          - profile: conda
-            path: modules/nf-core/deepvariant/makeexamples
-          - profile: conda
-            path: modules/nf-core/deepvariant/postprocessvariants
-          - profile: conda
-            path: modules/nf-core/deepvariant/rundeepvariant
-          - profile: conda
-            path: modules/nf-core/deepvariant/vcfstatsreport
-          - profile: conda
-            path: modules/nf-core/doubletdetection
-          - profile: conda
-            path: modules/nf-core/ensemblvep/vep
-          - profile: conda
-            path: modules/nf-core/fastk/fastk
-          - profile: conda
-            path: modules/nf-core/cellrangerarc/mkgtf
-          - profile: conda
-            path: modules/nf-core/fastk/histex
-          - profile: conda
-            path: modules/nf-core/fastk/merge
-          - profile: conda
-            path: modules/nf-core/fcs/fcsadaptor
-          - profile: conda
-            path: modules/nf-core/fcs/fcsgx
-          - profile: conda
-            path: modules/nf-core/ganon/buildcustom
-          - profile: conda
-            path: modules/nf-core/ganon/classify
-          - profile: conda
-            path: modules/nf-core/ganon/report
-          - profile: conda
-            path: modules/nf-core/ganon/table
-          - profile: conda
-            path: modules/nf-core/gatk4/cnnscorevariants
-          - profile: conda
-            path: modules/nf-core/gatk4/determinegermlinecontigploidy
-          - profile: conda
-            path: modules/nf-core/genescopefk
-          - profile: conda
-            path: modules/nf-core/ilastik/multicut
-          - profile: conda
-            path: modules/nf-core/ilastik/pixelclassification
-          - profile: conda
-            path: modules/nf-core/imputeme/vcftoprs
-          - profile: conda
-            path: modules/nf-core/mcstaging/imc2mc
-          - profile: conda
-            path: modules/nf-core/mcquant
-          - profile: conda
-            path: modules/nf-core/mcstaging/phenoimager2mc
-          - profile: conda
-            path: modules/nf-core/merquryfk/katcomp
-          - profile: conda
-            path: modules/nf-core/merquryfk/katgc
-          - profile: conda
-            path: modules/nf-core/merquryfk/merquryfk
-          - profile: conda
-            path: modules/nf-core/merquryfk/ploidyplot
-          - profile: conda
-            path: modules/nf-core/molkartgarage/clahe
-          - profile: conda
-            path: modules/nf-core/quartonotebook
-          - profile: conda
-            path: modules/nf-core/scimap/spatiallda
-          - profile: conda
-            path: modules/nf-core/sentieon/bwaindex
-          - profile: conda
-            path: modules/nf-core/sentieon/bwamem
-          - profile: conda
-            path: modules/nf-core/sentieon/datametrics
-          - profile: conda
-            path: modules/nf-core/sentieon/dedup
-          - profile: conda
-            path: modules/nf-core/sentieon/qualcal
-          - profile: conda
-            path: modules/nf-core/spaceranger/mkgtf
-          - profile: conda
-            path: modules/nf-core/spaceranger/mkref
-          - profile: conda
-            path: modules/nf-core/spaceranger/count
-          - profile: conda
-            path: modules/nf-core/spotiflow
-          - profile: conda
-            path: modules/nf-core/svanalyzer/svbenchmark
-          - profile: conda
-            path: modules/nf-core/universc
-          - profile: singularity
-            path: modules/nf-core/universc
-          - profile: conda
-            path: modules/nf-core/vt/decompose
-          - profile: singularity
-            path: modules/nf-core/bases2fastq
-          - profile: conda
-            path: modules/nf-core/wittyer
-          - profile: conda
-            path: modules/nf-core/islandpath
-          - profile: conda
-            path: modules/nf-core/scimap/mcmicro
-          - profile: conda
-            path: subworkflows/nf-core/vcf_annotate_ensemblvep
-          - profile: conda
-            path: subworkflows/nf-core/bcl_demultiplex
-          - profile: conda
-            path: subworkflows/nf-core/deepvariant
-          - profile: conda
-            path: subworkflows/nf-core/fastq_align_bamcmp_bwa
-          - profile: conda
-            path: subworkflows/nf-core/fastq_align_bwa
-          - profile: conda
-            path: subworkflows/nf-core/fasta_newick_epang_gappa
-          - path: modules/nf-core/parabricks/fq2bammeth
-          - path: modules/nf-core/parabricks/fq2bam
-          - path: modules/nf-core/parabricks/applybqsr
-          - profile: conda
-            path: modules/nf-core/xeniumranger/relabel
-          - profile: conda
-            path: modules/nf-core/xeniumranger/rename
-          - profile: conda
-            path: modules/nf-core/xeniumranger/resegment
-          - profile: conda
-            path: modules/nf-core/xeniumranger/import-segmentation
-
-    env:
-      NXF_ANSI_LOG: false
-
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-      - name: Run nf-test Action
-        uses: ./.github/actions/nf-test-action
-        with:
-          path: ${{ matrix.path }}
-          profile: ${{ matrix.profile }}
-
-  nf-test-gpu:
-    runs-on: "gpu"
-    name: nf-test-gpu
-    needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' && contains(needs.nf-test-changes.outputs.paths, 'modules/nf-core/parabricks') )
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-          - path: modules/nf-core/parabricks/applybqsr
-            profile: [docker_self_hosted, singularity]
-          - path: modules/nf-core/parabricks/fq2bam
-            profile: [docker_self_hosted, singularity]
-          - path: modules/nf-core/parabricks/fq2bammeth
-            profile: [docker_self_hosted, singularity]
-    env:
-      NXF_ANSI_LOG: false
-
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-      - name: Run nf-test Action
-        uses: ./.github/actions/nf-test-action
-        env:
-          SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
-          SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
-          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
-          SENTIEON_AUTH_MECH: "GitHub Actions - token"
-        with:
-          path: ${{ matrix.path }}
-          profile: ${{ matrix.profile }},gpu
-
-  confirm-pass:
-    runs-on: ubuntu-latest
-    needs:
-      [
-        prettier,
-        editorconfig,
-        pytest-changes,
-        nf-core-lint-modules,
-        nf-core-lint-subworkflows,
-        pytest,
-        nf-test-changes,
-        nf-test,
-        nf-test-gpu,
-      ]
-    if: always()
-    steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
-      - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: debug-print
-        if: always()
-        run: |
-          echo "toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index a86fd9bb10a..61d0d06a509 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -10,8 +10,12 @@ on:
 # TODO Skip testing CI if any changes to environment.yml
 
 env:
-  WAVE_VER: "1.5.0"
-  NFTEST_VER: "0.9.1"
+  # renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
+  WAVE_VERSION: "1.5.0"
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFTEST_VERSION: "0.9.1"
+  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+  NXF_VERSION: "24.10.1"
 
 jobs:
   generate-matrix:
@@ -62,8 +66,8 @@ jobs:
 
       - name: Install wave-cli
         run: |
-          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
-          sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
+          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
+          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
           chmod +x /usr/local/bin/wave
 
       - name: Build ${{ matrix.profile }} container
@@ -98,8 +102,8 @@ jobs:
 
       - name: Install wave-cli
         run: |
-          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
-          sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
+          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
+          sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
           chmod +x /usr/local/bin/wave
 
       - name: Create a registry name
@@ -139,7 +143,7 @@ jobs:
 
   #     - uses: nf-core/setup-nf-test@v1
   #       with:
-  #         version: ${{ env.NFTEST_VER }}
+  #         version: ${{ env.NFTEST_VERSION }}
 
   #     - name: Bump Snapshot Versions
   #       env:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b97fd79f3a8..b6517edd742 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -25,3 +25,8 @@ repos:
         files: \.py$
         args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
       - id: ruff-format # formatter
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.0.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
index 3dee85ffb4d..e00acce210f 100644
--- a/modules/nf-core/bowtie/align/main.nf
+++ b/modules/nf-core/bowtie/align/main.nf
@@ -5,7 +5,7 @@ process BOWTIE_ALIGN {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8c0819a9b1f520c49c933e667ae50de2a0730ece4c8b9efe79ac5e403963a9f/data' :
-        'community​.wave​.seqera​.io/library/bowtie_samtools:e1a14e1ce4e0170d' }"
+        'community.wave.seqera.io/library/bowtie_samtools:e1a14e1ce4e0170d' }"
 
     input:
     tuple val(meta), path(reads)
@@ -29,6 +29,7 @@ process BOWTIE_ALIGN {
     def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     """
     INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//')
+
     bowtie \\
         --threads $task.cpus \\
         --sam \\
diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test.snap b/modules/nf-core/bowtie/align/tests/main.nf.test.snap
index de95bb81531..e24eff79e62 100644
--- a/modules/nf-core/bowtie/align/tests/main.nf.test.snap
+++ b/modules/nf-core/bowtie/align/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - single_end": {
         "content": [
             [
-                "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
             ],
             [
                 "7bdcfc6f54ae6e8f4570395cc85db9a3"
@@ -27,10 +27,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-26T09:25:24.60746041"
+        "timestamp": "2024-11-14T10:55:41.588212"
     },
     "sarscov2 - single_end - stub": {
         "content": [
@@ -63,7 +63,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                    "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
                 ],
                 "bam": [
                     [
@@ -93,20 +93,20 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                    "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-25T10:00:28.666281812"
+        "timestamp": "2024-11-14T10:55:46.311312"
     },
     "sarscov2 - paired_end": {
         "content": [
             [
-                "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
             ],
             [
                 [
@@ -125,10 +125,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-26T11:57:56.604464368"
+        "timestamp": "2024-11-14T10:55:51.790156"
     },
     "sarscov2 - paired_end - stub": {
         "content": [
@@ -155,7 +155,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                    "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
                 ],
                 "bam": [
                     [
@@ -179,14 +179,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc"
+                    "versions.yml:md5,40a84d909e40d3b39ab6ed522cc75145"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-25T10:01:02.043164876"
+        "timestamp": "2024-11-14T10:55:56.594761"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf
index 0f6b9d4d1bf..953e12f6875 100644
--- a/modules/nf-core/bowtie/build/main.nf
+++ b/modules/nf-core/bowtie/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE_BUILD {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8c0819a9b1f520c49c933e667ae50de2a0730ece4c8b9efe79ac5e403963a9f/data' :
-        'community​.wave​.seqera​.io/library/bowtie_samtools:e1a14e1ce4e0170d' }"
+        'community.wave.seqera.io/library/bowtie_samtools:e1a14e1ce4e0170d' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test b/modules/nf-core/bowtie/build/tests/main.nf.test
index 81209a7b1fc..1811013d5ae 100644
--- a/modules/nf-core/bowtie/build/tests/main.nf.test
+++ b/modules/nf-core/bowtie/build/tests/main.nf.test
@@ -34,6 +34,7 @@ nextflow_process {
     test("sarscov2 - fasta - stub") {
 
         options "-stub"
+        tag "version"
         tag "stub"
 
         when {
@@ -56,4 +57,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test.snap b/modules/nf-core/bowtie/build/tests/main.nf.test.snap
index e8061756ba2..e71a80d922f 100644
--- a/modules/nf-core/bowtie/build/tests/main.nf.test.snap
+++ b/modules/nf-core/bowtie/build/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a"
+                    "versions.yml:md5,01c0299b236b1052f80f4be6aacfae6b"
                 ],
                 "index": [
                     [
@@ -36,15 +36,29 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a"
+                    "versions.yml:md5,01c0299b236b1052f80f4be6aacfae6b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-18T08:38:14.852528155"
+        "timestamp": "2024-11-14T10:56:03.634167"
+    },
+    "versions": {
+        "content": [
+            {
+                "BOWTIE_BUILD": {
+                    "bowtie": "1.3.1"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-10T11:48:00.007395903"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -65,7 +79,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a"
+                    "versions.yml:md5,01c0299b236b1052f80f4be6aacfae6b"
                 ],
                 "index": [
                     [
@@ -83,14 +97,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a"
+                    "versions.yml:md5,01c0299b236b1052f80f4be6aacfae6b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-18T08:37:53.65689025"
+        "timestamp": "2024-11-14T10:56:00.181902"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test
index c85fd447b3d..9cecef89358 100644
--- a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test
+++ b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test
@@ -8,6 +8,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "parabricks"
     tag "parabricks/applybqsr"
+    tag "gpu"
 
     test("sarscov2 - bam - pe") {
 
@@ -210,4 +211,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
index 8e4adb2966c..c2273e762ba 100644
--- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
+++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test
@@ -10,6 +10,7 @@ nextflow_process {
     tag "parabricks/fq2bam"
     tag "modules_nfcore"
     tag "parabricks"
+    tag "gpu"
 
     setup {
         run("BWA_INDEX") {
@@ -171,4 +172,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
index 42e436a3ba3..459eb6317db 100644
--- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
+++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
@@ -10,6 +10,7 @@ nextflow_process {
     tag "parabricks"
     tag "parabricks/fq2bammeth"
     tag "modules_nfcore"
+    tag "gpu"
 
     setup {
         run("BWAMETH_INDEX") {
@@ -119,4 +120,4 @@ nextflow_process {
             )
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/vcf2db/environment.yml b/modules/nf-core/vcf2db/environment.yml
index 58c477f9591..037e15309fd 100644
--- a/modules/nf-core/vcf2db/environment.yml
+++ b/modules/nf-core/vcf2db/environment.yml
@@ -1,5 +1,12 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
+  # renovate: datasource=conda depName=conda-forge/python
+  - conda-forge::python=2.7
+  # renovate: datasource=conda depName=bioconda/cyvcf2
+  - bioconda::cyvcf2=0.20.9
+  # renovate: datasource=conda depName=bioconda/vcf2db
   - bioconda::vcf2db=2020.02.24
diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf
index 56c26bb6c5f..9e050793e2d 100644
--- a/modules/nf-core/vcf2db/main.nf
+++ b/modules/nf-core/vcf2db/main.nf
@@ -5,8 +5,8 @@ process VCF2DB {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--pl5321hdfd78af_3':
-        'biocontainers/vcf2db:2020.02.24--pl5321hdfd78af_3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/14/14d1257c98f789e23a888e2961673b5b98d89e4d03e6a3efba2b1134ed439f61/data':
+        'community.wave.seqera.io/library/python_vcf2db:91f604106ada5cf2' }"
 
     input:
     tuple val(meta), path(vcf), path(ped)
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index c86fb134d75..f90c24c2bc8 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -43,5 +43,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.10.1'
 }
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index f651ff4d89d..fa21cb2edd6 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -32,12 +32,6 @@ profiles {
         docker.enabled = true
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
-    gpu {
-        docker.runOptions       = '-u $(id -u):$(id -g) --gpus device=0'
-        apptainer.runOptions    = '--no-mount tmp --writable-tmpfs --nv'
-        singularity.runOptions  = '--no-mount tmp --writable-tmpfs --nv'
-        use_gpu                 = true
-    }
     docker_self_hosted {
         docker.enabled = true
         docker.fixOwnership = true
@@ -62,5 +56,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.10.1'
 }