diff --git a/.github/nf-test-tags.yml b/.github/nf-test-tags.yml
new file mode 100644
index 0000000000..7e01f45416
--- /dev/null
+++ b/.github/nf-test-tags.yml
@@ -0,0 +1,54 @@
+exclude:
+  - tags: "bcftools/annotate"
+  - tags: "bcftools/concat"
+  - tags: "bcftools/mpileup"
+  - tags: "bcftools/sort"
+  - tags: "bwa/index"
+  - tags: "bwa/mem"
+  - tags: "bwamem2/index"
+  - tags: "bwamem2/mem"
+  - tags: "cat/cat"
+  - tags: "cat/fastq"
+  - tags: "cnvkit/antitarget"
+  - tags: "cnvkit/batch"
+  - tags: "cnvkit/reference"
+  - tags: "deepvariant"
+  - tags: "dragmap/align"
+  - tags: "dragmap/hashtable"
+  - tags: "ensemblvep/download"
+  - tags: "ensemblvep/vep"
+  - tags: "fastp"
+  - tags: "fastqc"
+  - tags: "fgbio/fastqtobam"
+  - tags: "freebayes"
+  - tags: "gatk4/applybqsr"
+  - tags: "gatk4/baserecalibrator"
+  - tags: "gatk4/estimatelibrarycomplexity"
+  - tags: "gatk4/genomicsdbimport"
+  - tags: "gatk4/haplotypecaller"
+  - tags: "gatk4/markduplicates"
+  - tags: "gatk4/mergevcfs"
+  - tags: "gatk4/mutect2"
+  - tags: "gatk4spark/applybqsr"
+  - tags: "gatk4spark/markduplicates"
+  - tags: "gawk"
+  - tags: "lofreq/callparallel"
+  - tags: "mosdepth"
+  - tags: "multiqc"
+  - tags: "ngscheckmate/ncm"
+  - tags: "samblaster"
+  - tags: "samtools/convert"
+  - tags: "samtools/mpileup"
+  - tags: "samtools/stats"
+  - tags: "snpeff/snpeff"
+  - tags: "strelka/germline"
+  - tags: "strelka/somatic"
+  - tags: "subworkflows/utils_nfvalidation_plugin"
+  - tags: "tabix/bgziptabix"
+  - tags: "tabix/tabix"
+  - tags: "tiddit/sv"
+  - tags: "untar"
+  - tags: "pipeline_sarek"
+include:
+  - tags: "pipeline_sarek"
+    profile: "test,docker"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d9999f5092..611f7595e9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,6 +14,10 @@ env:
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
+  SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -26,8 +30,9 @@ jobs:
       fail-fast: false
       matrix:
         shard: [1, 2, 3, 4, 5]
-        NXF_VER: ["latest-stable"] # TODO Test minimum version on release
+        NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
         profile: ["docker"]
+        filter: ["pipeline", "workflow"] # TODO Modules and Functions
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -52,14 +57,47 @@ jobs:
         with:
           version: ${{ env.NFT_VER }}
 
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - 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 "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python3 bin/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
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@v1.3.1
+
       - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
         run: |
           nf-test test \
               --ci \
+              --tap=test.tap \
+              --verbose \
               --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
               --changed-since HEAD^ \
               --profile "+${{ matrix.profile }}" \
-              --filter pipeline
+              --filter ${{ matrix.filter }}
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index bff41935bf..df63fce6f8 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -12,7 +12,6 @@ on:
       - dev
 
 env:
-  NFTEST_VER: "0.9.0"
   NXF_ANSI_LOG: false
   TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
   SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
@@ -189,170 +188,10 @@ jobs:
             !/home/ubuntu/pytest_workflow_*/*/work/singularity
             !${{ github.workspace }}/.singularity
 
-  nftest-changes:
-    name: Check for changes (nf-test)
-    runs-on: ubuntu-latest
-    outputs:
-      tags: ${{ steps.filter.outputs.changes }}
-
-    steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - name: Combine all tags.yml files
-        id: get_tags
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
-
-      - uses: frouioui/paths-filter@main
-        id: filter
-        with:
-          filters: ".github/tags.yml"
-          token: ""
-
-  nftest:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
-    runs-on: ubuntu-latest
-    needs: nftest-changes
-    if: needs.nftest-changes.outputs.tags != '[]'
-    strategy:
-      fail-fast: false
-      matrix:
-        tags: ["${{ fromJson(needs.nftest-changes.outputs.tags) }}"]
-        profile: ["docker"]
-        # profile: ["docker", "singularity", "conda"]
-        TEST_DATA_BASE:
-          - "test-datasets/data"
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        exclude:
-          - tags: "bcftools/annotate"
-          - tags: "bcftools/concat"
-          - tags: "bcftools/mpileup"
-          - tags: "bcftools/sort"
-          - tags: "bwa/index"
-          - tags: "bwa/mem"
-          - tags: "bwamem2/index"
-          - tags: "bwamem2/mem"
-          - tags: "cat/cat"
-          - tags: "cat/fastq"
-          - tags: "cnvkit/antitarget"
-          - tags: "cnvkit/batch"
-          - tags: "cnvkit/reference"
-          - tags: "deepvariant"
-          - tags: "dragmap/align"
-          - tags: "dragmap/hashtable"
-          - tags: "ensemblvep/download"
-          - tags: "ensemblvep/vep"
-          - tags: "fastp"
-          - tags: "fastqc"
-          - tags: "fgbio/fastqtobam"
-          - tags: "freebayes"
-          - tags: "gatk4/applybqsr"
-          - tags: "gatk4/baserecalibrator"
-          - tags: "gatk4/estimatelibrarycomplexity"
-          - tags: "gatk4/genomicsdbimport"
-          - tags: "gatk4/haplotypecaller"
-          - tags: "gatk4/markduplicates"
-          - tags: "gatk4/mergevcfs"
-          - tags: "gatk4/mutect2"
-          - tags: "gatk4spark/applybqsr"
-          - tags: "gatk4spark/markduplicates"
-          - tags: "gawk"
-          - tags: "lofreq/callparallel"
-          - tags: "mosdepth"
-          - tags: "multiqc"
-          - tags: "ngscheckmate/ncm"
-          - tags: "samblaster"
-          - tags: "samtools/convert"
-          - tags: "samtools/mpileup"
-          - tags: "samtools/stats"
-          - tags: "snpeff/snpeff"
-          - tags: "strelka/germline"
-          - tags: "strelka/somatic"
-          - tags: "subworkflows/utils_nfvalidation_plugin"
-          - tags: "tabix/bgziptabix"
-          - tags: "tabix/tabix"
-          - tags: "tiddit/sv"
-          - tags: "untar"
-          - tags: "pipeline_sarek"
-        include:
-          - tags: "pipeline_sarek"
-            profile: "test,docker"
-
-    steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
-      - name: Install Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFTEST_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          channels: conda-forge,bioconda
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-            # 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 "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python3 bin/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 $SENTIEON_AUTH_DATA_BASE64
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@v1.3.1
-
-      # Test the module
-      - name: Run nf-test
-        run: |
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tag ${{ matrix.tags }} \
-            --tap=test.tap \
-            --verbose
-
   confirm-pass:
     runs-on: ubuntu-latest
     needs:
       - pytest
-      - nftest
     if: always()
     steps:
       - name: All tests ok