diff --git a/.github/workflows/code-linting.yml b/.github/workflows/code-linting.yml
deleted file mode 100644
index 831453f8ea2..00000000000
--- a/.github/workflows/code-linting.yml
+++ /dev/null
@@ -1,43 +0,0 @@
-name: code-lint
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v3
-
-      - name: Install NodeJS
-        uses: actions/setup-node@v2
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check .
-
-  EditorConfig:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-node@v2
-
-      - 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)
diff --git a/.github/workflows/nf-core-linting.yml b/.github/workflows/nf-core-linting.yml
deleted file mode 100644
index 123decf27e6..00000000000
--- a/.github/workflows/nf-core-linting.yml
+++ /dev/null
@@ -1,83 +0,0 @@
-name: nf-core-lint
-run-name: nf-core-lint
-# This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-    name: check-changes
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-
-  lint:
-    runs-on: ubuntu-20.04
-    name: lint
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - name: Install pip
-        run: python -m pip install --upgrade pip
-
-      - name: Install nf-core tools
-        run: python -m pip install nf-core
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Lint ${{ matrix.tags }}
-        run: nf-core modules lint ${{ matrix.tags }}
-        # HACK
-        if: startsWith( matrix.tags, 'subworkflow' ) != true
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
deleted file mode 100644
index 57df4fef4c2..00000000000
--- a/.github/workflows/nf-test.yml
+++ /dev/null
@@ -1,182 +0,0 @@
-name: nf-test
-run-name: nf-test
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-    name: check-changes
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/nftest_modules.yml"
-
-  nf-test:
-    runs-on: ubuntu-20.04
-    name: nf-test
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-        profile: ["docker", "singularity", "conda"]
-        exclude:
-          - profile: "conda"
-            tags: annotsv
-          - profile: "conda"
-            tags: bases2fastq
-          - profile: "conda"
-            tags: bcl2fastq
-          - profile: "conda"
-            tags: bclconvert
-          - profile: "conda"
-            tags: cellranger/count
-          - profile: "conda"
-            tags: cellranger/mkfastq
-          - profile: "conda"
-            tags: cellranger/mkgtf
-          - profile: "conda"
-            tags: cellranger/mkref
-          - profile: "conda"
-            tags: deepvariant
-          - profile: "conda"
-            tags: ensemblvep/vep
-          - 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: "conda"
-            tags: genescopefk
-          - profile: "conda"
-            tags: ilastik/multicut
-          - profile: "conda"
-            tags: ilastik/pixelclassification
-          - profile: "conda"
-            tags: imputeme/vcftoprs
-          - profile: "conda"
-            tags: merquryfk/katcomp
-          - profile: "conda"
-            tags: merquryfk/katgc
-          - profile: "conda"
-            tags: merquryfk/merquryfk
-          - profile: "conda"
-            tags: merquryfk/ploidyplot
-          - profile: "conda"
-            tags: sentieon/bwaindex
-          - profile: "conda"
-            tags: sentieon/bwamem
-          - profile: "conda"
-            tags: universc
-          - profile: "singularity"
-            tags: universc
-          - profile: "conda"
-            tags: subworkflows/vcf_annotate_ensemblvep
-    env:
-      NXF_ANSI_LOG: false
-      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        if: env.SENTIEON_LICENSE_BASE64 != null
-        run: |
-          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
-          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
-          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
-          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
-          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
-
-      # Test the module
-      - name: Run nf-test
-        run: |
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tag ${{ matrix.tags }} \
-            --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
deleted file mode 100644
index dcfe6db7cf0..00000000000
--- a/.github/workflows/pytest-workflow.yml
+++ /dev/null
@@ -1,252 +0,0 @@
-name: pytest
-run-name: pytest
-on:
-  push:
-    branches: [master]
-  pull_request:
-    branches: [master]
-  merge_group:
-    types: [checks_requested]
-    branches: [master]
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  changes:
-    name: check-changes
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'modules' output variable
-      modules: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: dorny/paths-filter@v2
-        id: filter
-        with:
-          filters: "tests/config/pytest_modules.yml"
-
-  pytest:
-    runs-on: ubuntu-20.04
-    name: pytest
-    needs: changes
-    if: needs.changes.outputs.modules != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
-        profile: ["docker", "singularity", "conda"]
-        exclude:
-          - profile: "conda"
-            tags: annotsv
-          - profile: "conda"
-            tags: cellpose
-          - profile: "conda"
-            tags: mcquant
-          - profile: "conda"
-            tags: bases2fastq
-          - profile: "conda"
-            tags: backsub
-          - profile: "conda"
-            tags: basicpy
-          - profile: "conda"
-            tags: bcl2fastq
-          - profile: "conda"
-            tags: bclconvert
-          - profile: "conda"
-            tags: cellranger/count
-          - profile: "conda"
-            tags: cellranger/mkfastq
-          - profile: "conda"
-            tags: cellranger/mkgtf
-          - profile: "conda"
-            tags: cellranger/mkref
-          - profile: "conda"
-            tags: cellranger/mkvdjref
-          - profile: "conda"
-            tags: cellranger/multi
-          - profile: "conda"
-            tags: cellranger/vdj
-          - profile: "conda"
-            tags: coreograph
-          - profile: "conda"
-            tags: deepcell/mesmer
-          - profile: "conda"
-            tags: deepvariant
-          - 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/baserecalibratorspark
-          - profile: "conda"
-            tags: gatk4/cnnscorevariants
-          - profile: "conda"
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: "conda"
-            tags: gatk4/germlinecnvcaller
-          - profile: "conda"
-            tags: gatk4/markduplicatesspark
-          - profile: "conda"
-            tags: gatk4/postprocessgermlinecnvcalls
-          - profile: "conda"
-            tags: genescopefk
-          - profile: "conda"
-            tags: ilastik/multicut
-          - profile: "conda"
-            tags: ilastik/pixelclassification
-          - profile: "conda"
-            tags: imputeme/vcftoprs
-          - profile: "conda"
-            tags: merquryfk/katcomp
-          - profile: "conda"
-            tags: merquryfk/katgc
-          - profile: "conda"
-            tags: merquryfk/merquryfk
-          - profile: "conda"
-            tags: merquryfk/ploidyplot
-          - profile: "conda"
-            tags: mitohifi/findmitoreference
-          - profile: "conda"
-            tags: scimap/mcmicro
-          - profile: "conda"
-            tags: sentieon/applyvarcal
-          - profile: "conda"
-            tags: sentieon/bwaindex
-          - profile: "conda"
-            tags: sentieon/bwamem
-          - profile: "conda"
-            tags: sentieon/dedup
-          - profile: "conda"
-            tags: sentieon/gvcftyper
-          - profile: "conda"
-            tags: sentieon/haplotyper
-          - profile: "conda"
-            tags: sentieon/varcal
-          - profile: "conda"
-            tags: spaceranger/count
-          - profile: "conda"
-            tags: spaceranger/mkgtf
-          - profile: "conda"
-            tags: spaceranger/mkref
-          - profile: "conda"
-            tags: universc
-          - profile: "singularity"
-            tags: universc
-          - profile: "singularity"
-            tags: gatk4/determinegermlinecontigploidy
-          - profile: "conda"
-            tags: subworkflows/bcl_demultiplex
-          - profile: "conda"
-            tags: subworkflows/fasta_clean_fcs
-          - profile: "conda"
-            tags: islandpath
-    env:
-      NXF_ANSI_LOG: false
-      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow cryptography
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow
-        env:
-          CAPSULE_LOG: none
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        if: env.SENTIEON_LICENSE_BASE64 != null
-        run: |
-          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
-          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
-          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
-          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
-          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
-          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
-
-      # Test the module
-      - name: Run pytest-workflow
-        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
-
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt-get update > /dev/null
-          sudo apt-get install bat > /dev/null
-          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
-
-      - name: Setting global variables
-        uses: actions/github-script@v6
-        id: parsed
-        with:
-          script: |
-            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
-          result-encoding: string
-
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@v2
-        with:
-          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
-          path: |
-            /home/runner/pytest_workflow_*/*/.nextflow.log
-            /home/runner/pytest_workflow_*/*/log.out
-            /home/runner/pytest_workflow_*/*/log.err
-            /home/runner/pytest_workflow_*/*/work
-            !/home/runner/pytest_workflow_*/*/work/conda
-            !/home/runner/pytest_workflow_*/*/work/singularity
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 00000000000..f992ded1f68
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,522 @@
+name: test
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  merge_group:
+    types: [checks_requested]
+    branches: [master]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v3
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+
+      - 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:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  nf-core-lint:
+    runs-on: ubuntu-20.04
+    name: nf-core-lint
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        exclude:
+          - tags: "nf-test"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install nf-core tools
+        run: python -m pip install nf-core
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        # HACK
+        if: startsWith( matrix.tags, 'subworkflow' ) != true
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}
+
+  pytest:
+    runs-on: ubuntu-20.04
+    name: pytest
+    needs: [pytest-changes]
+    if: needs.pytest-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - tags: "nf-test"
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: cellpose
+          - profile: "conda"
+            tags: mcquant
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: backsub
+          - profile: "conda"
+            tags: basicpy
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: cellranger/mkvdjref
+          - profile: "conda"
+            tags: cellranger/multi
+          - profile: "conda"
+            tags: cellranger/vdj
+          - profile: "conda"
+            tags: coreograph
+          - profile: "conda"
+            tags: deepcell/mesmer
+          - profile: "conda"
+            tags: deepvariant
+          - 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/baserecalibratorspark
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: gatk4/germlinecnvcaller
+          - profile: "conda"
+            tags: gatk4/markduplicatesspark
+          - profile: "conda"
+            tags: gatk4/postprocessgermlinecnvcalls
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: mitohifi/findmitoreference
+          - profile: "conda"
+            tags: scimap/mcmicro
+          - profile: "conda"
+            tags: sentieon/applyvarcal
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: sentieon/dedup
+          - profile: "conda"
+            tags: sentieon/gvcftyper
+          - profile: "conda"
+            tags: sentieon/haplotyper
+          - profile: "conda"
+            tags: sentieon/varcal
+          - profile: "conda"
+            tags: spaceranger/count
+          - profile: "conda"
+            tags: spaceranger/mkgtf
+          - profile: "conda"
+            tags: spaceranger/mkref
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "singularity"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: subworkflows/bcl_demultiplex
+          - profile: "conda"
+            tags: subworkflows/fasta_clean_fcs
+          - profile: "conda"
+            tags: islandpath
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@v6
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
+
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/nftest_modules.yml"
+
+  nf-test:
+    runs-on: ubuntu-20.04
+    name: nf-test
+    needs: [nf-test-changes]
+    if: needs.nf-test-changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - tags: "nf-test"
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - 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: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    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/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
index c26d9aca9cf..44d83102dec 100644
--- a/modules/nf-core/bases2fastq/main.nf
+++ b/modules/nf-core/bases2fastq/main.nf
@@ -4,11 +4,6 @@ process BASES2FASTQ {
 
     container "nf-core/bases2fastq:1.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(run_manifest), path(run_dir)
 
@@ -26,6 +21,10 @@ process BASES2FASTQ {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def runManifest = run_manifest ? "-r ${run_manifest}" : ""
diff --git a/modules/nf-core/basicpy/main.nf b/modules/nf-core/basicpy/main.nf
index bfebe901ce8..cfcf9ac1ae8 100644
--- a/modules/nf-core/basicpy/main.nf
+++ b/modules/nf-core/basicpy/main.nf
@@ -2,11 +2,6 @@ process BASICPY {
     tag "$meta.id"
     label 'process_single'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "Basicpy module does not support Conda. Please use Docker / Singularity instead."
-    }
-
     container "docker.io/yfukai/basicpy-docker-mcmicro:0.2.1"
 
     input:
@@ -20,6 +15,10 @@ process BASICPY {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
@@ -33,6 +32,10 @@ process BASICPY {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
+    }
     """
     touch ${prefix}.-dfp.tiff
     touch ${prefix}.-dfp.tiff
diff --git a/modules/nf-core/bcl2fastq/main.nf b/modules/nf-core/bcl2fastq/main.nf
index 8bf02ddd8aa..1797bc67c76 100644
--- a/modules/nf-core/bcl2fastq/main.nf
+++ b/modules/nf-core/bcl2fastq/main.nf
@@ -4,11 +4,6 @@ process BCL2FASTQ {
 
     container "nf-core/bcl2fastq:2.20.0.422"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 
@@ -26,6 +21,10 @@ process BCL2FASTQ {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf
index 122950dca9c..2d8b7857df6 100644
--- a/modules/nf-core/bclconvert/main.nf
+++ b/modules/nf-core/bclconvert/main.nf
@@ -4,11 +4,6 @@ process BCLCONVERT {
 
     container "nf-core/bclconvert:4.0.3"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 
@@ -26,6 +21,10 @@ process BCLCONVERT {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
diff --git a/modules/nf-core/cellpose/main.nf b/modules/nf-core/cellpose/main.nf
index f0f462e0ff2..a2b2206923a 100644
--- a/modules/nf-core/cellpose/main.nf
+++ b/modules/nf-core/cellpose/main.nf
@@ -2,10 +2,6 @@ process CELLPOSE {
     tag "$meta.id"
     label 'process_medium'
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."}
-
     container "docker.io/biocontainers/cellpose:2.1.1_cv2"
 
     input:
@@ -20,6 +16,10 @@ process CELLPOSE {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def model_command = model ? "--pretrained_model $model" : ""
@@ -38,6 +38,10 @@ process CELLPOSE {
     END_VERSIONS
     """
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "2.1.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 0a76cbd4169..d7a191fc721 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_COUNT {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     tuple val(meta), path(reads, stageAs: "fastq_???/*")
     path  reference
@@ -21,11 +16,19 @@ process CELLRANGER_COUNT {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     template "cellranger_count.py"
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${prefix}/outs/"
diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf
index f57780afbf0..7a128edbd0b 100644
--- a/modules/nf-core/cellranger/mkfastq/main.nf
+++ b/modules/nf-core/cellranger/mkfastq/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKFASTQ {
 
     container "docker.io/nfcore/cellrangermkfastq:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path bcl
     path csv
@@ -21,6 +16,10 @@ process CELLRANGER_MKFASTQ {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
     """
@@ -38,6 +37,10 @@ process CELLRANGER_MKFASTQ {
     """
 
     stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
     """
     mkdir -p "${prefix}/outs/fastq_path/"
diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf
index 5411b0fdbfc..e0b0dd67e55 100644
--- a/modules/nf-core/cellranger/mkgtf/main.nf
+++ b/modules/nf-core/cellranger/mkgtf/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKGTF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path gtf
 
@@ -20,6 +15,10 @@ process CELLRANGER_MKGTF {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${gtf.baseName}.filtered"
     """
diff --git a/modules/nf-core/cellranger/mkref/main.nf b/modules/nf-core/cellranger/mkref/main.nf
index b4b9c547369..986891b8e48 100644
--- a/modules/nf-core/cellranger/mkref/main.nf
+++ b/modules/nf-core/cellranger/mkref/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKREF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path fasta
     path gtf
@@ -22,6 +17,10 @@ process CELLRANGER_MKREF {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     cellranger \\
diff --git a/modules/nf-core/cellranger/mkvdjref/main.nf b/modules/nf-core/cellranger/mkvdjref/main.nf
index 6d2ccc3949a..64e877f7e15 100644
--- a/modules/nf-core/cellranger/mkvdjref/main.nf
+++ b/modules/nf-core/cellranger/mkvdjref/main.nf
@@ -4,11 +4,6 @@ process CELLRANGER_MKVDJREF {
 
     container "nf-core/cellranger:7.1.0"
 
-    // Exit if running this module with -profile conda / -profile mamba
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
-    }
-
     input:
     path fasta
     path gtf
@@ -22,6 +17,10 @@ process CELLRANGER_MKVDJREF {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "CELLRANGER_MKVDJREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
     def args = task.ext.args ?: ''
     """
     cellranger \\
diff --git a/modules/nf-core/fcs/fcsgx/main.nf b/modules/nf-core/fcs/fcsgx/main.nf
index dc40a3fac74..de52886f2b3 100644
--- a/modules/nf-core/fcs/fcsgx/main.nf
+++ b/modules/nf-core/fcs/fcsgx/main.nf
@@ -3,8 +3,8 @@ process FCS_FCSGX {
     label 'process_low'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-gx.0.2.3.sif':
-        'docker.io/ncbi/fcs-gx:0.2.3' }"
+        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.4.0/fcs-gx.sif':
+        'docker.io/ncbi/fcs-gx:0.4.0' }"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -26,7 +26,7 @@ process FCS_FCSGX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FCSGX_VERSION = '0.2.3'
+    def FCSGX_VERSION = '0.4.0'
 
     """
     python3 /app/bin/run_gx \\
@@ -42,4 +42,20 @@ process FCS_FCSGX {
         FCS-GX: $FCSGX_VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def FCSGX_VERSION = '0.4.0'
+
+    """
+    mkdir -p out
+    touch out/${prefix}.fcs_gx_report.txt
+    touch out/${prefix}.taxonomy.rpt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python3 --version 2>&1 | sed -e "s/Python //g")
+        FCS-GX: $FCSGX_VERSION
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/kmcp/profile/main.nf b/modules/nf-core/kmcp/profile/main.nf
index cc520ef8907..a46721224b1 100644
--- a/modules/nf-core/kmcp/profile/main.nf
+++ b/modules/nf-core/kmcp/profile/main.nf
@@ -9,8 +9,7 @@ process KMCP_PROFILE {
 
     input:
     tuple val(meta), path(search_results)
-    path taxdump
-    path taxid
+    path (db)
     val mode
 
     output:
@@ -24,11 +23,13 @@ process KMCP_PROFILE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    taxid=`find -L ${db} -name "*map"`
+    taxdump=`find -L ${db}/*/ -type d  -not -name "R001"`
     kmcp \\
         profile \\
         $args \\
-        -X $taxdump \\
-        -T $taxid \\
+        -X \$taxdump \\
+        -T \$taxid \\
         -m $mode \\
         -j $task.cpus \\
         -o ${prefix}.profile \\
diff --git a/modules/nf-core/kmcp/profile/meta.yml b/modules/nf-core/kmcp/profile/meta.yml
index 512a882eab4..14f292c758e 100644
--- a/modules/nf-core/kmcp/profile/meta.yml
+++ b/modules/nf-core/kmcp/profile/meta.yml
@@ -23,18 +23,13 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - db:
+      type: directory
+      description: Database directory containing taxdump files and taxid file
   - search_results:
       type: file
       description: Gzipped file output from kmcp search module
       pattern: "*.gz"
-  - taxdump:
-      type: directory
-      description: Directory of NCBI taxonomy dump files - names.dmp, nodes.dmp
-      pattern: "*"
-  - taxid:
-      type: file
-      description: Tabular two-column file(s) mapping reference IDs to TaxIds.
-      pattern: "*.{csv,tsv}"
   - mode:
       type: integer
       description: Profiling mode.
diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf
index b0b5e960406..cb2d68435b7 100644
--- a/modules/nf-core/kmcp/search/main.nf
+++ b/modules/nf-core/kmcp/search/main.nf
@@ -40,8 +40,7 @@ process KMCP_SEARCH {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}
-    gzip ${prefix}
+    touch ${prefix}.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/kmcp/search/meta.yml b/modules/nf-core/kmcp/search/meta.yml
index d86ae8d172c..5526a179107 100644
--- a/modules/nf-core/kmcp/search/meta.yml
+++ b/modules/nf-core/kmcp/search/meta.yml
@@ -1,4 +1,4 @@
-name: "kmcp_compute"
+name: "kmcp_search"
 description: Search sequences against database
 keywords:
   - metagenomics
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 2f27c552f76..3a12336e73e 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -2045,10 +2045,18 @@ kmcp/index:
   - modules/nf-core/kmcp/index/**
   - tests/modules/nf-core/kmcp/index/**
 
+kmcp/merge:
+  - modules/nf-core/kmcp/merge/**
+  - tests/modules/nf-core/kmcp/merge/**
+
 kmcp/profile:
   - modules/nf-core/kmcp/profile/**
   - tests/modules/nf-core/kmcp/profile/**
 
+kmcp/search:
+  - modules/nf-core/kmcp/search/**
+  - tests/modules/nf-core/kmcp/search/**
+
 kofamscan:
   - modules/nf-core/kofamscan/**
   - tests/modules/nf-core/kofamscan/**
diff --git a/tests/modules/nf-core/bases2fastq/test.yml b/tests/modules/nf-core/bases2fastq/test.yml
index 88fe9c238da..9e2aa9ac129 100644
--- a/tests/modules/nf-core/bases2fastq/test.yml
+++ b/tests/modules/nf-core/bases2fastq/test.yml
@@ -5,14 +5,14 @@
   files:
     - path: output/bases2fastq/output/Bases2Fastq-Sim_QC.html
     - path: output/bases2fastq/output/Metrics.csv
-      md5sum: 0ec6da2b82e191098283474356024abf
+      md5sum: a8094b308b5653071ac029a27733e4a6
     - path: output/bases2fastq/output/RunManifest.json
       md5sum: a07dce8ee25c2a6f9355b677c26b53e2
     - path: output/bases2fastq/output/RunStats.json
     - path: output/bases2fastq/output/UnassignedSequences.csv
       md5sum: 11c1693830ce941b8cfb8d2431a59097
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
-      md5sum: 218abc70f61e8e8199a68f83ae836184
+      md5sum: 831c90ea31eff881e825cda691da77ae
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
-      md5sum: b95109bfb204daa150b61239d3368ee2
+      md5sum: e6c1f7ec00910ef195ff3d427c7a9f23
     - path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_stats.json
diff --git a/tests/modules/nf-core/kmcp/compute/main.nf b/tests/modules/nf-core/kmcp/compute/main.nf
index 73679ebae12..59860296890 100644
--- a/tests/modules/nf-core/kmcp/compute/main.nf
+++ b/tests/modules/nf-core/kmcp/compute/main.nf
@@ -19,7 +19,7 @@ workflow test_kmcp_compute_directory {
 
 input = UNTAR ( [
             [ id:'test' ],
-            file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp.tar.gz", checkIfExists: true)
+            file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/kmcp/kmcp_profile.tar.gz", checkIfExists: true)
         ]).untar
 
 KMCP_COMPUTE ( input )
diff --git a/tests/modules/nf-core/kmcp/compute/test.yml b/tests/modules/nf-core/kmcp/compute/test.yml
index e10ea1c2873..a8dbb2a24ee 100644
--- a/tests/modules/nf-core/kmcp/compute/test.yml
+++ b/tests/modules/nf-core/kmcp/compute/test.yml
@@ -1,8 +1,8 @@
 - name: kmcp compute test_kmcp_compute
   command: nextflow run ./tests/modules/nf-core/kmcp/compute -entry test_kmcp_compute -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/compute/nextflow.config
   tags:
-    - kmcp
     - kmcp/compute
+    - kmcp
   files:
     - path: output/kmcp/test_/_info.txt
       contains: ["#path	name	chunkIdx	idxNum	genomeSize	kmers"]
@@ -27,5 +27,4 @@
     - path: output/kmcp/test_/_info.txt
       contains: ["#path	name	chunkIdx	idxNum	genomeSize	kmers"]
     - path: output/kmcp/test_/genome.fasta.unik
-    - path: output/kmcp/test_/transcriptome.fasta.unik
     - path: output/kmcp/versions.yml
diff --git a/tests/modules/nf-core/kmcp/profile/main.nf b/tests/modules/nf-core/kmcp/profile/main.nf
index e41f4a2a7c1..bed70144213 100644
--- a/tests/modules/nf-core/kmcp/profile/main.nf
+++ b/tests/modules/nf-core/kmcp/profile/main.nf
@@ -10,23 +10,21 @@ include { KMCP_PROFILE } from '../../../../../modules/nf-core/kmcp/profile/main.
 
 workflow test_kmcp_profile {
 
-    input_compute = [
-        [ id:'test', single_end:false ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/NC_045512.2.fasta', checkIfExists: true)
-    ]
+    input_compute= UNTAR ( [
+            [ id:'test' ],
+            file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/kmcp/kmcp_profile.tar.gz", checkIfExists: true)
+        ]).untar
+
 
     input = [
         [ id:'test', single_end:true ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
     ]
 
-    taxdump =  [ [],file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/kmcp_profile.tar.gz', checkIfExists: true)]
-    ch_taxid = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/seqid2taxid.map', checkIfExists: true)
     mode = 3
 
-    UNTAR (taxdump)
-    KMCP_COMPUTE ( input_compute )
+    KMCP_COMPUTE (input_compute )
     KMCP_INDEX ( KMCP_COMPUTE.out.outdir )
     KMCP_SEARCH ( KMCP_INDEX.out.kmcp.map{it[1]}, input )
-    KMCP_PROFILE ( KMCP_SEARCH.out.result, UNTAR.out.untar.map{ it[1] }, ch_taxid, mode )
+    KMCP_PROFILE ( KMCP_SEARCH.out.result, input_compute.map{ it[1] }, mode )
 }
diff --git a/tests/modules/nf-core/kmcp/profile/nextflow.config b/tests/modules/nf-core/kmcp/profile/nextflow.config
index dafa8f3f73f..98a493be45f 100644
--- a/tests/modules/nf-core/kmcp/profile/nextflow.config
+++ b/tests/modules/nf-core/kmcp/profile/nextflow.config
@@ -2,7 +2,7 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: KMCP_INDEX {
+    withName: KMCP_COMPUTE {
         ext.prefix = { "${meta.id}_" }
     }
 
diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml
index 4d537bbd5ea..6dac88d16e3 100644
--- a/tests/modules/nf-core/kmcp/profile/test.yml
+++ b/tests/modules/nf-core/kmcp/profile/test.yml
@@ -1,17 +1,17 @@
 - name: kmcp profile test_kmcp_profile
   command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config
   tags:
-    - kmcp/profile
     - kmcp
+    - kmcp/profile
   files:
     - path: output/kmcp/test.profile
-    - path: output/untar/versions.yml
+    - path: output/kmcp/versions.yml
 
 - name: kmcp profile test_kmcp_profile stub_run
   command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config -stub-run
   tags:
-    - kmcp/profile
     - kmcp
+    - kmcp/profile
   files:
     - path: output/kmcp/test.profile
-    - path: output/untar/versions.yml
+    - path: output/kmcp/versions.yml
diff --git a/tests/modules/nf-core/kmcp/search/nextflow.config b/tests/modules/nf-core/kmcp/search/nextflow.config
index 4eb081d2033..dafa8f3f73f 100644
--- a/tests/modules/nf-core/kmcp/search/nextflow.config
+++ b/tests/modules/nf-core/kmcp/search/nextflow.config
@@ -6,8 +6,4 @@ process {
         ext.prefix = { "${meta.id}_" }
     }
 
-    withName: KMCP_SEARCH {
-        ext.prefix = { "${meta.id}_" }
-    }
-
 }
diff --git a/tests/modules/nf-core/kmcp/search/test.yml b/tests/modules/nf-core/kmcp/search/test.yml
index eb356e8755e..7669b72d494 100644
--- a/tests/modules/nf-core/kmcp/search/test.yml
+++ b/tests/modules/nf-core/kmcp/search/test.yml
@@ -4,9 +4,7 @@
     - kmcp
     - kmcp/search
   files:
-    - path: output/kmcp/test_/R001/__db.yml
-    - path: output/kmcp/test_/R001/__name_mapping.tsv
-    - path: output/kmcp/test_/R001/_block001.uniki
+    - path: output/kmcp/test.gz
     - path: output/kmcp/versions.yml
 
 - name: kmcp search test_kmcp_search stub_run
@@ -15,7 +13,5 @@
     - kmcp
     - kmcp/search
   files:
-    - path: output/kmcp/test_/R001/__db.yml
-    - path: output/kmcp/test_/R001/__name_mapping.tsv
-    - path: output/kmcp/test_/R001/_block001.uniki
+    - path: output/kmcp/test.gz
     - path: output/kmcp/versions.yml