diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 87f0345583a..877ac9c91da 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -76,8 +76,9 @@ jobs:
     name: pytest-changes
     runs-on: ubuntu-latest
     outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
+      tags: ${{ steps.filter.outputs.changes }}
+      modules: ${{ steps.tags.outputs.modules }}
+      subworkflows: ${{ steps.tags.outputs.subworkflows }}
     steps:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
@@ -90,36 +91,56 @@ jobs:
           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 matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
+      # 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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@v4
         with:
-          fetch-depth: 2 # To retrieve the preceding commit.
+          fetch-depth: 0
 
-      - name: Combine all tags.yml files
-        id: get_tags
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.3
+        with:
+          head: ${{ github.sha }}
+          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha }}
+          n_parents: 2
 
-      - name: debug
-        run: cat .github/tags.yml
+      - 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
 
-      # 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
-        with:
-          filters: ".github/tags.yml"
-          token: ""
+      - name: debug
+        run: |
+          echo ${{ steps.outputs.outputs.modules }}
+          echo ${{ steps.outputs.outputs.subworkflows }}
 
-  nf-core-lint:
+  nf-core-lint-modules:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
-    name: nf-core-lint
+    name: nf-core-lint-modules
     needs: [pytest-changes, nf-test-changes]
-    if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }}
+    if: ${{ (needs.pytest-changes.outputs.modules != '[]') || ( needs.nf-test-changes.outputs.modules != '[]') }}
     strategy:
       fail-fast: false
       matrix:
@@ -151,6 +172,7 @@ jobs:
         with:
           distribution: "temurin"
           java-version: "17"
+
       - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v2
 
@@ -159,25 +181,54 @@ jobs:
 
       - name: Lint module ${{ matrix.tags }}
         run: nf-core modules lint ${{ matrix.tags }}
-        if: ${{ !startsWith(matrix.tags, 'subworkflows/') }}
 
-      - name: Remove substring from matrix.tags
-        id: remove_substring
-        run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT
+  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@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - uses: actions/setup-java@v3
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
-      - name: Lint subworkflow ${{ matrix.tags }}
-        run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}}
-        if: ${{ startsWith(matrix.tags, 'subworkflows/') }}
+      - name: Lint module ${{ matrix.tags }}
+        run: nf-core subworkflows lint ${{ matrix.tags }}
 
   pytest:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
     name: pytest
     needs: [pytest-changes]
-    if: needs.pytest-changes.outputs.modules != '[]'
+    if: needs.pytest-changes.outputs.tags != '[]'
     strategy:
       fail-fast: false
       matrix:
-        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
         profile: [conda, docker, singularity]
         exclude:
           - tags: nf-test
@@ -370,6 +421,7 @@ jobs:
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
+
       - uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4
         id: cache-pip-pytest
         with:
@@ -465,130 +517,134 @@ jobs:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
     name: nf-test
     needs: [nf-test-changes]
-    if: needs.nf-test-changes.outputs.modules != '[]'
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
     strategy:
       fail-fast: false
       matrix:
-        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
-        profile: [conda, docker, singularity]
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [conda, docker_self_hosted, singularity]
         exclude:
-          - tags: nf-test
+          - path: modules/nf-core/nf-test
           - profile: conda
-            tags: angsd/gl
+            path: modules/nf-core/angsd/gl
           - profile: conda
-            tags: annotsv
+            path: modules/nf-core/annotsv
           - profile: conda
-            tags: happy/sompy
+            path: modules/nf-core/happy/sompy
           - profile: conda
-            tags: backsub
+            path: modules/nf-core/backsub
           - profile: conda
-            tags: bakta/bakta
+            path: modules/nf-core/bakta/bakta
           - profile: conda
-            tags: bakta/baktadbdownload
+            path: modules/nf-core/bakta/baktadbdownload
           - profile: conda
-            tags: bases2fastq
+            path: modules/nf-core/bases2fastq
           - profile: conda
-            tags: bcl2fastq
+            path: modules/nf-core/bcl2fastq
           - profile: conda
-            tags: bclconvert
+            path: modules/nf-core/bclconvert
           - profile: conda
-            tags: celesta
+            path: modules/nf-core/celesta
           - profile: conda
-            tags: cellpose
+            path: modules/nf-core/cellpose
           - profile: conda
-            tags: cellranger/count
+            path: modules/nf-core/cellranger/count
           - profile: conda
-            tags: cellranger/mkfastq
+            path: modules/nf-core/cellranger/mkfastq
           - profile: conda
-            tags: cellranger/mkgtf
+            path: modules/nf-core/cellranger/mkgtf
           - profile: conda
-            tags: cellranger/mkref
+            path: modules/nf-core/cellranger/mkref
           - profile: conda
-            tags: cellranger/mkvdjref
+            path: modules/nf-core/cellranger/mkvdjref
           - profile: conda
-            tags: cellranger/multi
+            path: modules/nf-core/cellranger/multi
           - profile: conda
-            tags: cellranger/vdj
+            path: modules/nf-core/cellranger/vdj
           - profile: conda
-            tags: custom/dumpsoftwareversions
+            path: modules/nf-core/custom/dumpsoftwareversions
           - profile: conda
-            tags: deepcell/mesmer
+            path: modules/nf-core/deepcell/mesmer
           - profile: conda
-            tags: deepvariant
+            path: modules/nf-core/deepvariant
           - profile: conda
-            tags: ensemblvep/vep
+            path: modules/nf-core/ensemblvep/vep
           - profile: conda
-            tags: fastk/fastk
+            path: modules/nf-core/fastk/fastk
           - profile: conda
-            tags: fastk/histex
+            path: modules/nf-core/fastk/histex
           - profile: conda
-            tags: fastk/merge
+            path: modules/nf-core/fastk/merge
           - profile: conda
-            tags: fcs/fcsadaptor
+            path: modules/nf-core/fcs/fcsadaptor
           - profile: conda
-            tags: fcs/fcsgx
+            path: modules/nf-core/fcs/fcsgx
           - profile: conda
-            tags: ganon/buildcustom
+            path: modules/nf-core/ganon/buildcustom
           - profile: conda
-            tags: ganon/classify
+            path: modules/nf-core/ganon/classify
           - profile: conda
-            tags: ganon/report
+            path: modules/nf-core/ganon/report
           - profile: conda
-            tags: ganon/table
+            path: modules/nf-core/ganon/table
           - profile: conda
-            tags: gatk4/cnnscorevariants
+            path: modules/nf-core/gatk4/cnnscorevariants
           - profile: conda
-            tags: gatk4/determinegermlinecontigploidy
+            path: modules/nf-core/gatk4/determinegermlinecontigploidy
           - profile: conda
-            tags: genescopefk
+            path: modules/nf-core/genescopefk
           - profile: conda
-            tags: ilastik/multicut
+            path: modules/nf-core/ilastik/multicut
           - profile: conda
-            tags: ilastik/pixelclassification
+            path: modules/nf-core/ilastik/pixelclassification
           - profile: conda
-            tags: imputeme/vcftoprs
+            path: modules/nf-core/imputeme/vcftoprs
           - profile: conda
-            tags: mcquant
+            path: modules/nf-core/mcquant
           - profile: conda
-            tags: merquryfk/katcomp
+            path: modules/nf-core/merquryfk/katcomp
           - profile: conda
-            tags: merquryfk/katgc
+            path: modules/nf-core/merquryfk/katgc
           - profile: conda
-            tags: merquryfk/merquryfk
+            path: modules/nf-core/merquryfk/merquryfk
           - profile: conda
-            tags: merquryfk/ploidyplot
+            path: modules/nf-core/merquryfk/ploidyplot
           - profile: conda
-            tags: molkartgarage/clahe
+            path: modules/nf-core/molkartgarage/clahe
           - profile: conda
-            tags: quartonotebook
+            path: modules/nf-core/quartonotebook
           - profile: conda
-            tags: scimap/spatiallda
+            path: modules/nf-core/scimap/spatiallda
           - profile: conda
-            tags: sentieon/bwaindex
+            path: modules/nf-core/sentieon/bwaindex
           - profile: conda
-            tags: sentieon/bwamem
+            path: modules/nf-core/sentieon/bwamem
           - profile: conda
-            tags: spaceranger/mkgtf
+            path: modules/nf-core/spaceranger/mkgtf
           - profile: conda
-            tags: spaceranger/mkref
+            path: modules/nf-core/spaceranger/mkref
           - profile: conda
-            tags: spaceranger/count
+            path: modules/nf-core/spaceranger/count
           - profile: conda
-            tags: svanalyzer/svbenchmark
+            path: modules/nf-core/svanalyzer/svbenchmark
           - profile: conda
-            tags: universc
+            path: modules/nf-core/universc
           - profile: singularity
-            tags: universc
+            path: modules/nf-core/universc
           - profile: conda
-            tags: vt/decompose
-          - profile: conda
-            tags: subworkflows/vcf_annotate_ensemblvep
+            path: modules/nf-core/vt/decompose
           - profile: singularity
-            tags: bases2fastq
+            path: modules/nf-core/bases2fastq
           - profile: conda
-            tags: wittyer
+            path: modules/nf-core/wittyer
           - profile: conda
-            tags: islandpath
+            path: modules/nf-core/islandpath
+          - profile: conda
+            path: subworkflows/nf-core/vcf_annotate_ensemblvep
+          - profile: conda
+            path: subworkflows/nf-core/fastq_align_bamcmp_bwa
+          - profile: conda
+            path: subworkflows/nf-core/fastq_align_bwa
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
@@ -638,7 +694,6 @@ jobs:
           miniconda-version: "latest"
           auto-update-conda: true
           channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
 
       - name: Conda setup
         run: |
@@ -675,10 +730,10 @@ jobs:
 
           NFT_WORKDIR=~ \
           nf-test test \
-            --profile=$PROFILE \
-            --tag ${{ matrix.tags }} \
+            --profile=${{ matrix.profile }} \
             --tap=test.tap \
-            --verbose
+            --verbose \
+            ${{ matrix.path }}
 
       - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
         with:
@@ -692,7 +747,17 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    needs:
+      [
+        prettier,
+        editorconfig,
+        pytest-changes,
+        nf-core-lint-modules,
+        nf-core-lint-subworkflows,
+        pytest,
+        nf-test-changes,
+        nf-test,
+      ]
     if: always()
     steps:
       - name: All tests ok