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) }}"