From 6839ad25747603cc2f3a1a3f64ac7948f85eddac Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 13:46:42 -0500
Subject: [PATCH 01/51] ci: Copy over from methylseq

---
 .github/workflows/ci.yml     | 369 ++++-------------------------------
 .github/workflows/pytest.yml | 369 +++++++++++++++++++++++++++++++++++
 2 files changed, 403 insertions(+), 335 deletions(-)
 create mode 100644 .github/workflows/pytest.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4252b0d63c..d9999f5092 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,369 +1,68 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
+  push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
-  merge_group:
-    types:
-      - checks_requested
-    branches:
-      - master
-      - 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 }}
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+  NFT_VER: "0.9.0"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
-# Cancel if a newer run is started
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  pytest-changes:
-    name: Check for changes (pytest)
-    runs-on: ubuntu-latest
-    outputs:
-      # Expose matched filters as job 'tags' output variable
-      tags: ${{ steps.filter.outputs.changes }}
-    steps:
-      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - uses: frouioui/paths-filter@main
-        id: filter
-        with:
-          filters: "tests/config/pytesttags.yml"
-          token: ""
-
-  pytest:
-    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+  test:
     runs-on: ubuntu-latest
-    needs: pytest-changes
-    if: needs.pytest-changes.outputs.tags != '[]'
     strategy:
       fail-fast: false
       matrix:
-        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
+        shard: [1, 2, 3, 4, 5]
+        NXF_VER: ["latest-stable"] # TODO Test minimum version on release
         profile: ["docker"]
-        # profile: ["docker", "singularity", "conda"]
-        TEST_DATA_BASE:
-          - "test-datasets/data"
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-        exclude:
-          - tags: "sentieon/bwamem"
-          - tags: "sentieon/dedup"
-          - tags: "sentieon/dnascope"
-          - tags: "sentieon/dnascope_joint_germline"
-          - tags: "sentieon/dnascope_skip_filter"
-          - tags: "sentieon/haplotyper"
-          - tags: "sentieon/haplotyper_joint_germline"
-          - tags: "sentieon/haplotyper_skip_filter"
-          - NXF_VER: "latest-everything"
-            tags: "joint_germline"
-
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-
-      - name: Hash Github Workspace
-        id: hash_workspace
-        run: |
-          echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
-
-      - name: Set up Python
-        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
-        with:
-          python-version: "3.11"
-          cache: "pip"
-          cache-dependency-path: |
-            **/requirements.txt
-
-      - name: Install Python dependencies
-        run: pip install --upgrade -r tests/requirements.txt
-
-      - name: Install Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up miniconda
-        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
-
-      - name: Cache test data
-        id: cache-testdata
-        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
-          path: test-datasets/
-          key: ${{ steps.hash_workspace.outputs.digest }}
+          fetch-depth: 0
 
-      - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true'
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+      - uses: actions/setup-python@v4
         with:
-          repository: nf-core/test-datasets
-          ref: sarek3
-          path: test-datasets/
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in tests/csv/3.0/*csv; do
-            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
-
-      # 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 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 $SENTIEON_AUTH_DATA_BASE64
-
-      - name: Conda clean
-        if: matrix.profile == 'conda'
-        run: conda clean -a
-
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@v1.3.1
-
-      - name: Run pytest-workflow
-        uses: Wandalen/wretry.action@v1
-        with:
-          command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
-          attempt_limit: 3
+          python-version: "3.11"
+          architecture: "x64"
 
-      - name: Output log on failure
-        if: failure()
+      - name: Install pdiff to see diff between nf-test snapshots
         run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+          python -m pip install --upgrade pip
+          pip install pdiff
 
-      - name: Upload logs on failure
-        if: failure()
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4
-        with:
-          name: logs-${{ matrix.profile }}
-          path: |
-            /home/ubuntu/pytest_workflow_*/*/.nextflow.log
-            /home/ubuntu/pytest_workflow_*/*/log.out
-            /home/ubuntu/pytest_workflow_*/*/log.err
-            /home/ubuntu/pytest_workflow_*/*/work
-            !/home/ubuntu/pytest_workflow_*/*/work/conda
-            !/home/ubuntu/pytest_workflow_*/*/work/singularity
-            !${{ github.workspace }}/.singularity
-
-  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 ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v2
+      - uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
+      - uses: nf-core/setup-nf-test@v1
         with:
-          version: ${{ env.NFTEST_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
+          version: ${{ env.NFT_VER }}
 
-      - 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
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
         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
-        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) }}"
+              --ci \
+              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}" \
+              --filter pipeline
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
new file mode 100644
index 0000000000..bff41935bf
--- /dev/null
+++ b/.github/workflows/pytest.yml
@@ -0,0 +1,369 @@
+name: pytest-workflow
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  pull_request:
+  release:
+    types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
+
+env:
+  NFTEST_VER: "0.9.0"
+  NXF_ANSI_LOG: false
+  TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
+  SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest-changes:
+    name: Check for changes (pytest)
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - uses: frouioui/paths-filter@main
+        id: filter
+        with:
+          filters: "tests/config/pytesttags.yml"
+          token: ""
+
+  pytest:
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    runs-on: ubuntu-latest
+    needs: pytest-changes
+    if: needs.pytest-changes.outputs.tags != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"]
+        profile: ["docker"]
+        # profile: ["docker", "singularity", "conda"]
+        TEST_DATA_BASE:
+          - "test-datasets/data"
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+        exclude:
+          - tags: "sentieon/bwamem"
+          - tags: "sentieon/dedup"
+          - tags: "sentieon/dnascope"
+          - tags: "sentieon/dnascope_joint_germline"
+          - tags: "sentieon/dnascope_skip_filter"
+          - tags: "sentieon/haplotyper"
+          - tags: "sentieon/haplotyper_joint_germline"
+          - tags: "sentieon/haplotyper_skip_filter"
+          - NXF_VER: "latest-everything"
+            tags: "joint_germline"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        with:
+          python-version: "3.11"
+          cache: "pip"
+          cache-dependency-path: |
+            **/requirements.txt
+
+      - name: Install Python dependencies
+        run: pip install --upgrade -r tests/requirements.txt
+
+      - name: Install Nextflow ${{ matrix.NXF_VER }}
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up miniconda
+        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
+
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        with:
+          path: test-datasets/
+          key: ${{ steps.hash_workspace.outputs.digest }}
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
+        with:
+          repository: nf-core/test-datasets
+          ref: sarek3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in tests/csv/3.0/*csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
+      # 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 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 $SENTIEON_AUTH_DATA_BASE64
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@v1.3.1
+
+      - name: Run pytest-workflow
+        uses: Wandalen/wretry.action@v1
+        with:
+          command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+          attempt_limit: 3
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4
+        with:
+          name: logs-${{ matrix.profile }}
+          path: |
+            /home/ubuntu/pytest_workflow_*/*/.nextflow.log
+            /home/ubuntu/pytest_workflow_*/*/log.out
+            /home/ubuntu/pytest_workflow_*/*/log.err
+            /home/ubuntu/pytest_workflow_*/*/work
+            !/home/ubuntu/pytest_workflow_*/*/work/conda
+            !/home/ubuntu/pytest_workflow_*/*/work/singularity
+            !${{ github.workspace }}/.singularity
+
+  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
+        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) }}"

From 6fdf0379031b57e2c93e78a0e79f074482c60975 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 13:55:17 -0500
Subject: [PATCH 02/51] ci: Move Sarek specific settings to ci

---
 .github/nf-test-tags.yml     |  54 ++++++++++++
 .github/workflows/ci.yml     |  42 ++++++++-
 .github/workflows/pytest.yml | 161 -----------------------------------
 3 files changed, 94 insertions(+), 163 deletions(-)
 create mode 100644 .github/nf-test-tags.yml

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

From ac87c356c9fb47e4c824e366520dd798b21fa742 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 14:01:01 -0500
Subject: [PATCH 03/51] ci: tap => xml

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 611f7595e9..05da504c39 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -92,7 +92,7 @@ jobs:
         run: |
           nf-test test \
               --ci \
-              --tap=test.tap \
+              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
               --verbose \
               --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
               --changed-since HEAD^ \
@@ -100,7 +100,7 @@ jobs:
               --filter ${{ matrix.filter }}
 
       - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always() # always run even if the previous step fails
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
         with:
-          report_paths: test.xml
+          report_paths: "TEST-*.xml"

From 50b9c886c0f93e0fe26856e5e99d0b406bbd80a4 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 14:43:54 -0500
Subject: [PATCH 04/51] build: Add triggers

---
 nf-test.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf-test.config b/nf-test.config
index 208636eda6..a2f1f5b8ad 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,6 +3,7 @@ config {
     workDir ".nf-test"
     configFile "conf/test.config"
     profile "test"
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'conf/test_full.config'
 
     plugins {
         load "nft-utils@0.0.1"

From 277c7fa02ab7957da97423dc40a269c7ccb2f370 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 15:01:47 -0500
Subject: [PATCH 05/51] ci: Add clean up

---
 .github/workflows/ci.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 05da504c39..eacba5ab62 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -104,3 +104,8 @@ jobs:
         if: success() || failure() # always run even if the previous step fails
         with:
           report_paths: "TEST-*.xml"
+
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/

From fb36aa8ea6ee5cea3b73a9e9ef0ef2b48aeec52d Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 15:03:39 -0500
Subject: [PATCH 06/51] ci: Give jobs a name

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index eacba5ab62..633ee4dbb4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -26,13 +26,14 @@ concurrency:
 jobs:
   test:
     runs-on: ubuntu-latest
+    name: ${{ matrix.NXF_VER }} | ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}
     strategy:
       fail-fast: false
       matrix:
-        shard: [1, 2, 3, 4, 5]
         NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
-        profile: ["docker"]
         filter: ["pipeline", "workflow"] # TODO Modules and Functions
+        profile: ["docker"]
+        shard: [1, 2, 3, 4, 5]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

From ca0cfc3b8923bd5c89315afa937d76f10fce89e0 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 15:08:45 -0500
Subject: [PATCH 07/51] ci: job-total => 5

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 633ee4dbb4..170509c395 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -89,13 +89,13 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+      - name: Run Tests (Shard ${{ matrix.shard }}/5)
         run: |
           nf-test test \
               --ci \
               --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
               --verbose \
-              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
+              --shard ${{ matrix.shard }}/5 \
               --changed-since HEAD^ \
               --profile "+${{ matrix.profile }}" \
               --filter ${{ matrix.filter }}

From 06f22b657d0b0ee75abeabcae1b81143e307dbf5 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 15:17:29 -0500
Subject: [PATCH 08/51] ci: Follow dependencies

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 170509c395..14fef6b3b1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
-        filter: ["pipeline", "workflow"] # TODO Modules and Functions
+        filter: ["pipeline", "workflow", "process"] # TODO Functions
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
     steps:
@@ -97,6 +97,7 @@ jobs:
               --verbose \
               --shard ${{ matrix.shard }}/5 \
               --changed-since HEAD^ \
+              --follow-dependencies \
               --profile "+${{ matrix.profile }}" \
               --filter ${{ matrix.filter }}
 

From fcec8fab670456357c2c974800b6af1ba46c1bf2 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 1 Oct 2024 15:19:03 -0500
Subject: [PATCH 09/51] ci: Wondering if we can combine proccesses and
 functions

To save runners
---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 14fef6b3b1..f1ac073348 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
-        filter: ["pipeline", "workflow", "process"] # TODO Functions
+        filter: ["pipeline", "workflow", "process,function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
     steps:

From f44ffa339d8efd47a81d002c18ba443cef491d6b Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Wed, 2 Oct 2024 09:34:28 -0500
Subject: [PATCH 10/51] test: Manually nump software versions txt

---
 tests/main.nf.test.snap | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
index 7ce873964c..1fe8c40ab9 100644
--- a/tests/main.nf.test.snap
+++ b/tests/main.nf.test.snap
@@ -143,7 +143,7 @@
                 "multiqc_citations.txt:md5,4660dd5d8757841ed75dca3a90d21617",
                 "multiqc_fastqc.txt:md5,bde0d0bffa62228b33fb68b7e25b6ff8",
                 "multiqc_samtools_stats.txt:md5,0f1e4c6c497d9a952765f9f3068ea4b9",
-                "multiqc_software_versions.txt:md5,2c9d16da278a231b0dc4c4cb5c08e626",
+                "multiqc_software_versions.txt:md5,c596381071f4245cf706dc2aed5ee1a9",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -173,4 +173,4 @@
         },
         "timestamp": "2024-10-01T10:33:51.201431"
     }
-}
\ No newline at end of file
+}

From 5187cc1e84de7c53907b7cd69f0f457f1630ddbc Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Wed, 2 Oct 2024 09:35:50 -0500
Subject: [PATCH 11/51] ci: Run processes and functions seperately

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f1ac073348..c69fd23642 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
-        filter: ["pipeline", "workflow", "process,function"]
+        filter: ["pipeline", "workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
     steps:

From ee7107fc6c4ea26a5d899c6cc5d88317f67fea2a Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Wed, 2 Oct 2024 10:06:47 -0500
Subject: [PATCH 12/51] ci(#1672): Remove latest-everything

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c69fd23642..6cde7f0201 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,7 +30,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release
+        # BUG: "latest-everything" https://github.com/nf-core/sarek/issues/1672
+        NXF_VER: ["23.04.0"] # TODO Test minimum version on release
         filter: ["pipeline", "workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]

From 89d1b07cc8864f09018c3e405d8e2aa76aacfbdd Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:04:59 +0200
Subject: [PATCH 13/51] Update .github/workflows/ci.yml

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3c3d3d7724..fcab02aeca 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -30,8 +30,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # BUG: "latest-everything" https://github.com/nf-core/sarek/issues/1672
-        NXF_VER: ["23.04.0"] # TODO Test minimum version on release
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
         filter: ["pipeline", "workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]

From 9edd171339dee9e0ee6416bb4f04551e5489c13b Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:08:47 +0200
Subject: [PATCH 14/51] Update .github/nf-test-tags.yml

---
 .github/nf-test-tags.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/nf-test-tags.yml b/.github/nf-test-tags.yml
index 7e01f45416..1c4f61b4d4 100644
--- a/.github/nf-test-tags.yml
+++ b/.github/nf-test-tags.yml
@@ -48,7 +48,3 @@ exclude:
   - tags: "tabix/tabix"
   - tags: "tiddit/sv"
   - tags: "untar"
-  - tags: "pipeline_sarek"
-include:
-  - tags: "pipeline_sarek"
-    profile: "test,docker"

From bf661f42980840f028043cbedfb903783f43aa5d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:26:29 +0200
Subject: [PATCH 15/51] no need for tags

---
 tests/main.nf.test | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/main.nf.test b/tests/main.nf.test
index 748e4df596..ab497d52fa 100644
--- a/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -2,8 +2,6 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-    tag "pipeline"
-    tag "pipeline_sarek"
 
     test("Run with profile test") {
 

From 8386f980b0458901543ab72f9daacb91f3052fe0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:41:14 +0200
Subject: [PATCH 16/51] just 1 shard for pipeline as we have just 1 test
 currently

---
 .github/workflows/ci.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fcab02aeca..2e3e4aaf39 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -26,16 +26,19 @@ concurrency:
 jobs:
   test:
     runs-on: ubuntu-latest
-    name: ${{ matrix.NXF_VER }} | ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}
+    name: "${{ matrix.NXF_VER }} | ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}"
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        filter: ["pipeline", "workflow", "process", "function"]
+        filter: ["workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
+        include:
+          - filter: "pipeline"
+            shard: [1]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

From 6924616aa19a5f1b2a37a32dc0e28f1801965217 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:43:42 +0200
Subject: [PATCH 17/51] just 1 shard for pipeline as we have just 1 test
 currently

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2e3e4aaf39..f0d0dae03d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,12 +33,12 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        filter: ["workflow", "process", "function"]
+        filter: ["pipeline", "workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
-        include:
+        exclude:
           - filter: "pipeline"
-            shard: [1]
+            shard: [2, 3, 4, 5]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

From 304198c5ddd78ff2874dffa05a0e8ba2dec740ad Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 09:46:03 +0200
Subject: [PATCH 18/51] just 1 shard for pipeline as we have just 1 test
 currently

---
 .github/workflows/ci.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f0d0dae03d..0718a79ce7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,7 +38,13 @@ jobs:
         shard: [1, 2, 3, 4, 5]
         exclude:
           - filter: "pipeline"
-            shard: [2, 3, 4, 5]
+            shard: 2
+          - filter: "pipeline"
+            shard: 3
+          - filter: "pipeline"
+            shard: 4
+          - filter: "pipeline"
+            shard: 5
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

From bea4da624f87ea99680bab4cf3691577936cbe05 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 10:26:04 +0200
Subject: [PATCH 19/51] fix samplesheet_to_channel test

---
 .../local/samplesheet_to_channel/main.nf.test | 34 ----------
 .../samplesheet_to_channel/tests/main.nf.test | 62 +++++++++++++++++++
 .../{ => tests}/main.nf.test.snap             | 22 ++++---
 3 files changed, 75 insertions(+), 43 deletions(-)
 delete mode 100644 subworkflows/local/samplesheet_to_channel/main.nf.test
 create mode 100644 subworkflows/local/samplesheet_to_channel/tests/main.nf.test
 rename subworkflows/local/samplesheet_to_channel/{ => tests}/main.nf.test.snap (55%)

diff --git a/subworkflows/local/samplesheet_to_channel/main.nf.test b/subworkflows/local/samplesheet_to_channel/main.nf.test
deleted file mode 100644
index 49eeb2a132..0000000000
--- a/subworkflows/local/samplesheet_to_channel/main.nf.test
+++ /dev/null
@@ -1,34 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow SAMPLESHEET_TO_CHANNEL"
-    script "subworkflows/local/samplesheet_to_channel/main.nf"
-    workflow "SAMPLESHEET_TO_CHANNEL"
-
-    test("Should run without failures") {
-
-        when {
-            params {
-                // define parameters here. Example:
-                skip_tools = 'baserecalibrator'
-
-            }
-            workflow {
-                """
-                // define inputs of the workflow here. Example:
-                input[0] = Channel.of([['patient':'test', 'sample':'test',
-                                        'sex':'XX', 'status':0, 'lane':'test_L1'],
-                                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-                                        [], [], [], [], [], [], []])
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert snapshot(workflow.out).match()
-        }
-
-    }
-
-}
diff --git a/subworkflows/local/samplesheet_to_channel/tests/main.nf.test b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test
new file mode 100644
index 0000000000..e1c8682d27
--- /dev/null
+++ b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test
@@ -0,0 +1,62 @@
+nextflow_workflow {
+
+    name "Test Workflow SAMPLESHEET_TO_CHANNEL"
+    script "../main.nf"
+    workflow "SAMPLESHEET_TO_CHANNEL"
+
+    test("Should run without failures") {
+        when {
+            params {
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                input[0] = Channel.of([
+                    ['patient':'test', 'sample':'test',
+                    'sex':'XX', 'status':0, 'lane':'test_L1'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    [], [], [], [], [], [], [], [], []
+                ])
+                input[1] = 'bwa-mem' // aligner
+                input[2] = [] // ascat_alleles
+                input[3] = [] // ascat_loci
+                input[4] = [] // ascat_loci_gc
+                input[5] = [] // ascat_loci_rt
+                input[6] = [] // bcftools_annotations
+                input[7] = [] // bcftools_annotations_tbi
+                input[8] = [] // bcftools_header_lines
+                input[9] = false // build_only_index
+                input[10] = [] // dbsnp
+                input[11] = [] // fasta
+                input[12] = [] // germline_resource
+                input[13] = [] // intervals
+                input[14] = false // joint_germline
+                input[15] = false // joint_mutect2
+                input[16] = [] // known_indels
+                input[17] = [] // known_snps
+                input[18] = false // no_intervals
+                input[19] = [] // pon
+                input[20] = 'variant' // sentieon_dnascope_emit_mode
+                input[21] = 'variant' // sentieon_haplotyper_emit_mode
+                input[22] = '' // seq_center
+                input[23] = 'ILLUMINA' // seq_platform
+                input[24] = 'baserecalibrator' // skip_tools
+                input[25] = [] // snpeff_cache
+                input[26] = 'WBcel235.105' // snpeff_db
+                input[27] = 'mapping' // step
+                input[28] = 'strelka' // tools
+                input[29] = [] // umi_read_structure
+                input[30] = false // wes
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(workflow.out).match()
+        }
+
+    }
+
+}
diff --git a/subworkflows/local/samplesheet_to_channel/main.nf.test.snap b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test.snap
similarity index 55%
rename from subworkflows/local/samplesheet_to_channel/main.nf.test.snap
rename to subworkflows/local/samplesheet_to_channel/tests/main.nf.test.snap
index fa440f539b..758041c999 100644
--- a/subworkflows/local/samplesheet_to_channel/main.nf.test.snap
+++ b/subworkflows/local/samplesheet_to_channel/tests/main.nf.test.snap
@@ -9,15 +9,15 @@
                             "sample": "test",
                             "sex": "XX",
                             "status": 0,
+                            "lane": "test_L1",
                             "id": "test-test_L1",
+                            "data_type": "fastq_gz",
                             "num_lanes": 1,
-                            "read_group": "\"@RG\\tID:null.test.test_L1\\tPU:test_L1\\tSM:test_test\\tLB:test\\tDS:null\\tPL:ILLUMINA\"",
-                            "data_type": "fastq",
                             "size": 1
                         },
                         [
-                            "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz",
-                            "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
+                            "/ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz",
+                            "/ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
                         ]
                     ]
                 ],
@@ -28,20 +28,24 @@
                             "sample": "test",
                             "sex": "XX",
                             "status": 0,
+                            "lane": "test_L1",
                             "id": "test-test_L1",
+                            "data_type": "fastq_gz",
                             "num_lanes": 1,
-                            "read_group": "\"@RG\\tID:null.test.test_L1\\tPU:test_L1\\tSM:test_test\\tLB:test\\tDS:null\\tPL:ILLUMINA\"",
-                            "data_type": "fastq",
                             "size": 1
                         },
                         [
-                            "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz",
-                            "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
+                            "/ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz",
+                            "/ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
                         ]
                     ]
                 ]
             }
         ],
-        "timestamp": "2023-10-16T14:12:54.640503"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.09.0"
+        },
+        "timestamp": "2024-10-04T10:25:14.620549"
     }
 }
\ No newline at end of file

From 1304a7ce75024f0dbedff20a459d63dc903c282a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 14:54:31 +0200
Subject: [PATCH 20/51] update all modules/subworkflows

---
 modules.json                                  |  30 ++--
 modules/nf-core/bcftools/concat/main.nf       |  16 +-
 modules/nf-core/bcftools/concat/meta.yml      |  27 ++-
 .../bcftools/concat/tests/main.nf.test        |  18 +-
 .../bcftools/concat/tests/main.nf.test.snap   | 158 +++++++++---------
 modules/nf-core/gatk4/applybqsr/main.nf       |  13 ++
 .../gatk4/applybqsr/tests/main.nf.test        |  59 +++++++
 .../gatk4/applybqsr/tests/main.nf.test.snap   |  78 +++++++++
 .../gatk4/gatherpileupsummaries/main.nf       |  11 ++
 .../gatherpileupsummaries/tests/main.nf.test  |  25 +++
 .../tests/main.nf.test.snap                   |  35 ++++
 .../sentieon/applyvarcal/environment.yml      |   2 +-
 modules/nf-core/sentieon/applyvarcal/main.nf  |   4 +-
 .../nf-core/sentieon/bwamem/environment.yml   |   2 +-
 modules/nf-core/sentieon/bwamem/main.nf       |   4 +-
 .../sentieon/bwamem/tests/main.nf.test.snap   |  50 +++---
 .../nf-core/sentieon/dedup/environment.yml    |   2 +-
 modules/nf-core/sentieon/dedup/main.nf        |   4 +-
 .../sentieon/dedup/tests/main.nf.test.snap    |  56 +++----
 .../sentieon/dnamodelapply/environment.yml    |   2 +-
 .../nf-core/sentieon/dnamodelapply/main.nf    |   4 +-
 .../nf-core/sentieon/dnascope/environment.yml |   2 +-
 modules/nf-core/sentieon/dnascope/main.nf     |   4 +-
 .../sentieon/gvcftyper/environment.yml        |   2 +-
 modules/nf-core/sentieon/gvcftyper/main.nf    |   4 +-
 .../gvcftyper/tests/main.nf.test.snap         |  38 ++---
 .../sentieon/haplotyper/environment.yml       |   2 +-
 modules/nf-core/sentieon/haplotyper/main.nf   |   4 +-
 .../haplotyper/tests/main.nf.test.snap        |  50 +++---
 .../nf-core/sentieon/varcal/environment.yml   |   2 +-
 modules/nf-core/sentieon/varcal/main.nf       |   4 +-
 modules/nf-core/tabix/bgziptabix/main.nf      |   5 +-
 .../tabix/bgziptabix/tests/main.nf.test       |  29 ++++
 .../tabix/bgziptabix/tests/main.nf.test.snap  |  73 ++++++--
 .../nf-core/utils_nextflow_pipeline/main.nf   |  24 ++-
 .../tests/nextflow.config                     |   2 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  45 +++--
 .../tests/main.nf.test                        |   2 +-
 38 files changed, 596 insertions(+), 296 deletions(-)

diff --git a/modules.json b/modules.json
index 96ff1b1cba..1bb6c3ab13 100644
--- a/modules.json
+++ b/modules.json
@@ -18,7 +18,7 @@
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                         "installed_by": ["modules"]
                     },
                     "bcftools/mpileup": {
@@ -181,7 +181,7 @@
                     },
                     "gatk4/applybqsr": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6b3bf38285d94cc1ea3cd9fa93310d54b04c3819",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applyvqsr": {
@@ -231,7 +231,7 @@
                     },
                     "gatk4/gatherpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "679f45cae4f603f12d7c38c042afee11150574a0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genomicsdbimport": {
@@ -406,42 +406,42 @@
                     },
                     "sentieon/applyvarcal": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/bwamem": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dedup": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnamodelapply": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnascope": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/gvcftyper": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/haplotyper": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/varcal": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "snpeff/download": {
@@ -476,7 +476,7 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
                         "installed_by": ["modules", "vcf_annotate_snpeff"]
                     },
                     "tabix/tabix": {
@@ -515,17 +515,17 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "1f19c093c86ae49d1899e234d4aa4d56c57be780",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_annotate_ensemblvep": {
diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
index e2337eff25..a94b28d86d 100644
--- a/modules/nf-core/bcftools/concat/main.nf
+++ b/modules/nf-core/bcftools/concat/main.nf
@@ -11,18 +11,22 @@ process BCFTOOLS_CONCAT {
     tuple val(meta), path(vcfs), path(tbi)
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
-    tuple val(meta), path("*.tbi"), emit: tbi, optional: true
-    tuple val(meta), path("*.csi"), emit: csi, optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("${prefix}.vcf.gz")    , emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true
+    path  "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name }
+    def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n    ")
     """
+    ${create_input_index}
+
     bcftools concat \\
         --output ${prefix}.vcf.gz \\
         $args \\
@@ -37,7 +41,7 @@ process BCFTOOLS_CONCAT {
 
     stub:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
     def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
                 args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
                 args.contains("--write-index") || args.contains("-W") ? "csi" :
diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml
index b5d1f5b2ce..d2565b289f 100644
--- a/modules/nf-core/bcftools/concat/meta.yml
+++ b/modules/nf-core/bcftools/concat/meta.yml
@@ -37,9 +37,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.gz":
-          type: file
-          description: VCF concatenated output file
+          pattern: "*.{vcf.gz}"
+      - ${prefix}.vcf.gz:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.{vcf.gz}"
   - tbi:
       - meta:
@@ -47,9 +50,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.tbi":
-          type: file
-          description: Alternative VCF file index
+          pattern: "*.tbi"
+      - ${prefix}.vcf.gz.tbi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.tbi"
   - csi:
       - meta:
@@ -57,9 +63,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.csi":
-          type: file
-          description: Default VCF file index
+          pattern: "*.csi"
+      - ${prefix}.vcf.gz.csi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.csi"
   - versions:
       - versions.yml:
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test
index cea386e3bd..cb4642b29c 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "bcftools/concat"
 
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") {
 
         config "./nextflow.config"
 
@@ -41,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
@@ -78,7 +78,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
@@ -115,7 +115,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
@@ -153,7 +153,7 @@ nextflow_process {
     }
 
 
-    test("sarscov2 - [[vcf1, vcf2], []]") {
+    test("homo_sapiens - [[vcf1, vcf2], []]") {
 
         config "./nextflow.config"
 
@@ -181,7 +181,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
 
         config "./nextflow.config"
         options "-stub"
@@ -213,7 +213,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -246,7 +246,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -279,7 +279,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
index 1182854f94..09e87cd3e5 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": {
         "content": [
             {
                 "0": [
@@ -49,12 +49,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T08:09:13.734103412"
+        "timestamp": "2024-09-26T11:04:11.178539482"
     },
-    "sarscov2 - [[vcf1, vcf2], []]": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": {
         "content": [
             {
                 "0": [
@@ -94,12 +94,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:09.213249578"
+        "timestamp": "2024-09-26T11:03:08.765639958"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
         "content": [
             [
                 [
@@ -125,12 +125,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T08:08:23.981388325"
+        "timestamp": "2024-09-26T11:03:21.607274757"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
         "content": [
             {
                 "0": [
@@ -142,29 +142,29 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "2": [
+                    
                 ],
                 "3": [
                     "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
                 ],
                 "csi": [
+                    
+                ],
+                "tbi": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "tbi": [
-                    
                 ],
                 "vcf": [
                     [
@@ -180,12 +180,43 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-26T11:04:27.332133878"
+    },
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test3"
+                    },
+                    "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test3"
+                    },
+                    "test3_vcf.vcf.gz.csi"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:01:24.419027693"
+        "timestamp": "2024-09-26T11:03:36.575719606"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": {
+    "homo_sapiens - [[vcf1, vcf2], []]": {
         "content": [
             {
                 "0": [
@@ -225,43 +256,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:03.597061078"
+        "timestamp": "2024-09-26T11:03:54.069826178"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test3"
-                    },
-                    "test3_vcf.vcf.gz.csi"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-05T14:00:10.868487669"
-    },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
             {
                 "0": [
@@ -301,12 +301,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-04T15:19:14.836256897"
+        "timestamp": "2024-09-26T11:04:02.45346063"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": {
         "content": [
             [
                 [
@@ -332,12 +332,12 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:00:31.061411617"
+        "timestamp": "2024-09-26T11:03:44.618596639"
     },
-    "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
+    "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": {
         "content": [
             {
                 "0": [
@@ -349,29 +349,29 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "2": [
-                    
                 ],
                 "3": [
                     "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659"
                 ],
                 "csi": [
-                    
-                ],
-                "tbi": [
                     [
                         {
                             "id": "test3"
                         },
-                        "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "tbi": [
+                    
                 ],
                 "vcf": [
                     [
@@ -387,9 +387,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-06-05T14:01:35.209746508"
+        "timestamp": "2024-09-26T11:04:19.745768656"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf
index 78db9d7f00..4e91c311b0 100644
--- a/modules/nf-core/gatk4/applybqsr/main.nf
+++ b/modules/nf-core/gatk4/applybqsr/main.nf
@@ -48,4 +48,17 @@ process GATK4_APPLYBQSR {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_extension = input.getExtension()
+    def output_extension = input_extension == 'bam' ? 'bam' : 'cram'
+    """
+    touch ${prefix}.${output_extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test
index 3d9c6204f7..acb41ce1e4 100644
--- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test
+++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test
@@ -92,4 +92,63 @@ nextflow_process {
         }
     }
 
+    test("sarscov2 - cram - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true),
+                    []
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap
index a387039d6a..19b37d0636 100644
--- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap
@@ -1,4 +1,43 @@
 {
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "cram": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T10:25:00.314573"
+    },
     "sarscov2 - bam - intervals": {
         "content": [
             {
@@ -60,6 +99,45 @@
         },
         "timestamp": "2023-12-09T03:10:46.70859771"
     },
+    "sarscov2 - cram - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
+                ],
+                "bam": [
+                    
+                ],
+                "cram": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T10:24:52.761169"
+    },
     "sarscov2 - bam": {
         "content": [
             {
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
index c784d59ab2..bcafd544b4 100644
--- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
@@ -44,4 +44,15 @@ process GATK4_GATHERPILEUPSUMMARIES {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pileups.table
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test
index 8497e64db3..f33c6a0d94 100644
--- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test
@@ -34,4 +34,29 @@ nextflow_process {
         }
     }
 
+    test("test-gatk4-gatherpileupsummaries - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ]
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap
index f05a7ef0d1..fd9f258344 100644
--- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap
@@ -1,4 +1,39 @@
 {
+    "test-gatk4-gatherpileupsummaries - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.out.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T10:44:42.759098"
+    },
     "test-gatk4-gatherpileupsummaries": {
         "content": [
             {
diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/applyvarcal/environment.yml
+++ b/modules/nf-core/sentieon/applyvarcal/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf
index 9f64f5a2f3..724912d689 100644
--- a/modules/nf-core/sentieon/applyvarcal/main.nf
+++ b/modules/nf-core/sentieon/applyvarcal/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_APPLYVARCAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/bwamem/environment.yml
+++ b/modules/nf-core/sentieon/bwamem/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
index 76e364deca..c038a857bf 100644
--- a/modules/nf-core/sentieon/bwamem/main.nf
+++ b/modules/nf-core/sentieon/bwamem/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_BWAMEM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap
index 0dc67a9a5b..77070ccc45 100644
--- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap
@@ -8,12 +8,12 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.bam:md5,58bc2194d084cf8462a3a7f6114c303a",
-                        "test.bam.bai:md5,4fd9b026ff2306cc292cd695e11d5628"
+                        "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b",
+                        "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ],
                 "bam_and_bai": [
                     [
@@ -21,12 +21,12 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.bam:md5,58bc2194d084cf8462a3a7f6114c303a",
-                        "test.bam.bai:md5,4fd9b026ff2306cc292cd695e11d5628"
+                        "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b",
+                        "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ]
             }
         ],
@@ -34,7 +34,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-19T08:58:40.112926615"
+        "timestamp": "2024-10-02T10:25:33.275731212"
     },
     "Paired-End - stub": {
         "content": [
@@ -50,7 +50,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ],
                 "bam_and_bai": [
                     [
@@ -63,7 +63,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ]
             }
         ],
@@ -71,7 +71,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-19T08:59:20.476791905"
+        "timestamp": "2024-10-02T10:26:16.58588651"
     },
     "Paired-End": {
         "content": [
@@ -82,12 +82,12 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,3418d864f42215d1c0c8d604d9571b0d",
+                        "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268",
                         "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ],
                 "bam_and_bai": [
                     [
@@ -95,12 +95,12 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bam:md5,3418d864f42215d1c0c8d604d9571b0d",
+                        "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268",
                         "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ]
             }
         ],
@@ -108,7 +108,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-19T08:59:00.346034062"
+        "timestamp": "2024-10-02T10:25:55.068934639"
     },
     "Single-End - stub": {
         "content": [
@@ -124,7 +124,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ],
                 "bam_and_bai": [
                     [
@@ -137,7 +137,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ]
             }
         ],
@@ -145,7 +145,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-19T08:59:10.054146084"
+        "timestamp": "2024-10-02T10:26:05.151760076"
     },
     "Single-End Output CRAM": {
         "content": [
@@ -156,12 +156,12 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.cram:md5,04d88bd709dc0bc27ca81a09e80d4a1b",
-                        "test.cram.crai:md5,ac34c713fe95aa8a1fd6291bdbb76dcf"
+                        "test.cram:md5,817cf0847ae0c89062e2ee4be312101a",
+                        "test.cram.crai:md5,60f801c550a18982e55207adb31ec351"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ],
                 "bam_and_bai": [
                     [
@@ -169,12 +169,12 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.cram:md5,04d88bd709dc0bc27ca81a09e80d4a1b",
-                        "test.cram.crai:md5,ac34c713fe95aa8a1fd6291bdbb76dcf"
+                        "test.cram:md5,817cf0847ae0c89062e2ee4be312101a",
+                        "test.cram.crai:md5,60f801c550a18982e55207adb31ec351"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6095ad80036c5d876c2616504a21efcc"
+                    "versions.yml:md5,755d24c7416c1408313ec93814cef759"
                 ]
             }
         ],
@@ -182,6 +182,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-19T08:58:49.962693499"
+        "timestamp": "2024-10-02T10:25:44.360755915"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/dedup/environment.yml
+++ b/modules/nf-core/sentieon/dedup/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
index f0b387f64f..5735df7340 100644
--- a/modules/nf-core/sentieon/dedup/main.nf
+++ b/modules/nf-core/sentieon/dedup/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_DEDUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap
index c1cd83ec34..26117a7cdf 100644
--- a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram:md5,d2993113f4614f5196fc74d489412fc4"
+                        "test.cram:md5,e46e97256846338e1cff32d862105491"
                     ]
                 ],
                 "1": [
@@ -34,7 +34,7 @@
                         {
                             "id": "test"
                         },
-                        "test.score:md5,a97459ff2939682091bac3c3912402dc"
+                        "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b"
                     ]
                 ],
                 "5": [
@@ -42,7 +42,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics:md5,ccd45ea1f2397184e3ab271b1ba8bb2a"
+                        "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc"
                     ]
                 ],
                 "6": [
@@ -50,11 +50,11 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics.multiqc.tsv:md5,ccd45ea1f2397184e3ab271b1ba8bb2a"
+                        "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc"
                     ]
                 ],
                 "7": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ],
                 "bai": [
                     [
@@ -80,7 +80,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram:md5,d2993113f4614f5196fc74d489412fc4"
+                        "test.cram:md5,e46e97256846338e1cff32d862105491"
                     ]
                 ],
                 "metrics": [
@@ -88,7 +88,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics:md5,ccd45ea1f2397184e3ab271b1ba8bb2a"
+                        "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc"
                     ]
                 ],
                 "metrics_multiqc_tsv": [
@@ -96,7 +96,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics.multiqc.tsv:md5,ccd45ea1f2397184e3ab271b1ba8bb2a"
+                        "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc"
                     ]
                 ],
                 "score": [
@@ -104,19 +104,19 @@
                         {
                             "id": "test"
                         },
-                        "test.score:md5,a97459ff2939682091bac3c3912402dc"
+                        "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-26T13:02:23.640202"
+        "timestamp": "2024-10-02T10:28:10.570152622"
     },
     "Test removing duplicates": {
         "content": [
@@ -126,7 +126,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram:md5,e67398ab64430191f9d15cb8a8f425c7"
+                        "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4"
                     ]
                 ],
                 "1": [
@@ -153,7 +153,7 @@
                         {
                             "id": "test"
                         },
-                        "test.score:md5,a97459ff2939682091bac3c3912402dc"
+                        "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b"
                     ]
                 ],
                 "5": [
@@ -161,7 +161,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics:md5,7fc2ddc6b21838bdc42aff146549cea2"
+                        "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65"
                     ]
                 ],
                 "6": [
@@ -169,11 +169,11 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics.multiqc.tsv:md5,7fc2ddc6b21838bdc42aff146549cea2"
+                        "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65"
                     ]
                 ],
                 "7": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ],
                 "bai": [
                     [
@@ -199,7 +199,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram:md5,e67398ab64430191f9d15cb8a8f425c7"
+                        "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4"
                     ]
                 ],
                 "metrics": [
@@ -207,7 +207,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics:md5,7fc2ddc6b21838bdc42aff146549cea2"
+                        "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65"
                     ]
                 ],
                 "metrics_multiqc_tsv": [
@@ -215,7 +215,7 @@
                         {
                             "id": "test"
                         },
-                        "test.cram.metrics.multiqc.tsv:md5,7fc2ddc6b21838bdc42aff146549cea2"
+                        "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65"
                     ]
                 ],
                 "score": [
@@ -223,19 +223,19 @@
                         {
                             "id": "test"
                         },
-                        "test.score:md5,a97459ff2939682091bac3c3912402dc"
+                        "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-26T13:02:33.698037"
+        "timestamp": "2024-10-02T10:28:19.377946074"
     },
     "Test stub": {
         "content": [
@@ -292,7 +292,7 @@
                     ]
                 ],
                 "7": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ],
                 "bai": [
                     [
@@ -346,14 +346,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e"
+                    "versions.yml:md5,763463853476be96846b6da5aecfacf4"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-26T13:02:41.360148"
+        "timestamp": "2024-10-02T10:28:28.792696026"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/dnamodelapply/environment.yml
+++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf
index b4b10ce4d0..85fd601b39 100644
--- a/modules/nf-core/sentieon/dnamodelapply/main.nf
+++ b/modules/nf-core/sentieon/dnamodelapply/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_DNAMODELAPPLY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(vcf), path(idx)
diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/dnascope/environment.yml
+++ b/modules/nf-core/sentieon/dnascope/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf
index 63d7d23b8a..bdeb62521a 100644
--- a/modules/nf-core/sentieon/dnascope/main.nf
+++ b/modules/nf-core/sentieon/dnascope/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_DNASCOPE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(intervals)
diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/gvcftyper/environment.yml
+++ b/modules/nf-core/sentieon/gvcftyper/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
index e2e5d2434d..6817c6dbe2 100644
--- a/modules/nf-core/sentieon/gvcftyper/main.nf
+++ b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_GVCFTYPER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(gvcfs), path(tbis), path(intervals)
diff --git a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap
index 5e7e40fb6b..627b62fd87 100644
--- a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap
@@ -2,58 +2,58 @@
     "sentieon gvcftyper dbsnp": {
         "content": [
             [
-                "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
             ],
             "test.genotyped.vcf.gz.tbi",
             "21606383c760bf676d4c1f747b97d118"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:12:47.508154"
+        "timestamp": "2024-10-02T10:29:01.102534193"
     },
     "sentieon gvcftyper dbsnp intervals": {
         "content": [
             [
-                "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
             ],
             "test.genotyped.vcf.gz.tbi",
             "21606383c760bf676d4c1f747b97d118"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:13:05.636172"
+        "timestamp": "2024-10-02T10:29:20.933217951"
     },
     "sentieon gvcftyper vcf.gz": {
         "content": [
             [
-                "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
             ],
             "test.genotyped.vcf.gz.tbi",
             "d13216836f1452e200b215b796606671"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:12:38.720056"
+        "timestamp": "2024-10-02T10:28:50.937002394"
     },
     "sentieon gvcftyper intervals": {
         "content": [
             [
-                "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
             ],
             "test.genotyped.vcf.gz.tbi",
             "d13216836f1452e200b215b796606671"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:12:56.700687"
+        "timestamp": "2024-10-02T10:29:11.029924476"
     },
     "sentieon gvcftyper - stub": {
         "content": [
@@ -75,7 +75,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                    "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
                 ],
                 "vcf_gz": [
                     [
@@ -94,28 +94,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                    "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:03:46.379477"
+        "timestamp": "2024-10-02T10:29:30.788262037"
     },
     "sentieon gvcftyper vcf": {
         "content": [
             [
-                "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b"
+                "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a"
             ],
             "test.genotyped.vcf.gz.tbi",
             "d13216836f1452e200b215b796606671"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T14:12:29.24482"
+        "timestamp": "2024-10-02T10:28:41.276698125"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/haplotyper/environment.yml
+++ b/modules/nf-core/sentieon/haplotyper/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf
index 33122d86b2..a04b342caf 100644
--- a/modules/nf-core/sentieon/haplotyper/main.nf
+++ b/modules/nf-core/sentieon/haplotyper/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_HAPLOTYPER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals), path(recal_table)
diff --git a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap
index 5b77a02f5e..0527f0fcbe 100644
--- a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap
+++ b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap
@@ -2,49 +2,49 @@
     "Sentieon Haplotyper VCF": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.unfiltered.vcf.gz.tbi",
             "cea0045051da7877b38a1e25df812a91"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:16:51.711057"
+        "timestamp": "2024-10-02T10:29:42.675527558"
     },
     "Sentieon Haplotyper Recalibration": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.unfiltered.vcf.gz.tbi",
             "10faa3b669c49826098e09784d8a4716"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T15:21:57.012186"
+        "timestamp": "2024-10-02T10:30:38.708688756"
     },
     "Sentieon Haplotyper GVCF": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.g.vcf.gz.tbi",
             "338fc3c37b208d6595948576833eb665"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:17:01.797501"
+        "timestamp": "2024-10-02T10:29:53.99302993"
     },
     "Sentieon Haplotyper BOTH": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.g.vcf.gz.tbi",
             "338fc3c37b208d6595948576833eb665",
@@ -53,14 +53,14 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:17:12.021226"
+        "timestamp": "2024-10-02T10:30:03.323463525"
     },
     "Sentieon Haplotyper DBSNP BOTH": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.g.vcf.gz.tbi",
             "228556b7921205f023fec51098feeb97",
@@ -69,14 +69,14 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:30:48.065511"
+        "timestamp": "2024-10-02T10:30:25.917634004"
     },
     "Sentieon Haplotyper Intervals BOTH": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.g.vcf.gz.tbi",
             "338fc3c37b208d6595948576833eb665",
@@ -85,9 +85,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:17:22.554336"
+        "timestamp": "2024-10-02T10:30:14.249175276"
     },
     "Sentieon Haplotyper - stub": {
         "content": [
@@ -125,7 +125,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                    "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
                 ],
                 "gvcf": [
                     [
@@ -160,28 +160,28 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                    "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T10:47:33.117516"
+        "timestamp": "2024-10-02T10:30:56.435076872"
     },
     "Sentieon Haplotyper multiple CRAMs": {
         "content": [
             [
-                "versions.yml:md5,b58c15c81619894cdbab1f2edf694190"
+                "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877"
             ],
             "test.unfiltered.vcf.gz.tbi",
             "b5d6e09e336438e38f7bf5531799e3a"
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-13T17:04:30.67684393"
+        "timestamp": "2024-10-02T10:30:49.266709749"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml
index 185d95bde8..d7abf668ea 100644
--- a/modules/nf-core/sentieon/varcal/environment.yml
+++ b/modules/nf-core/sentieon/varcal/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::sentieon=202308.02
+  - bioconda::sentieon=202308.03
diff --git a/modules/nf-core/sentieon/varcal/main.nf b/modules/nf-core/sentieon/varcal/main.nf
index 7c85c12102..d78eacb44a 100644
--- a/modules/nf-core/sentieon/varcal/main.nf
+++ b/modules/nf-core/sentieon/varcal/main.nf
@@ -5,8 +5,8 @@ process SENTIEON_VARCAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
-        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' :
+        'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index 05041f4953..22f37a7739 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def args2 = task.ext.args2 ?: ''
+    def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi"
     """
     echo "" | gzip > ${prefix}.${input.getExtension()}.gz
-    touch ${prefix}.${input.getExtension()}.gz.tbi
-    touch ${prefix}.${input.getExtension()}.gz.csi
+    touch ${prefix}.${input.getExtension()}.gz.${index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
index 1a84d74fc0..4d4130dc07 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test
@@ -91,4 +91,33 @@ nextflow_process {
 
     }
 
+    test("sarscov2_bed_tbi_stub") {
+        config "./tabix_tbi.config"
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ],
+                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.gz_tbi[0][1]).name
+                                ).match("tbi_stub")
+                }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
index c166ea7288..fb87799b20 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -91,6 +91,47 @@
         },
         "timestamp": "2024-02-19T14:51:00.548801"
     },
+    "sarscov2_bed_tbi_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
+                ],
+                "gz_csi": [
+                    
+                ],
+                "gz_tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-25T14:45:18.533169949"
+    },
     "csi_stub": {
         "content": [
             "test.bed.gz"
@@ -101,6 +142,16 @@
         },
         "timestamp": "2024-02-19T14:51:09.218454"
     },
+    "tbi_stub": {
+        "content": [
+            "test.bed.gz"
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-25T14:45:18.550930179"
+    },
     "tbi_test": {
         "content": [
             "tbi_test.bed.gz"
@@ -115,13 +166,7 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
                     [
@@ -145,13 +190,7 @@
                     ]
                 ],
                 "gz_tbi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                        "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
@@ -159,9 +198,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-19T11:29:45.105209991"
+        "timestamp": "2024-09-25T14:44:19.786135972"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f66..28e32b200e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6d..a09572e5bb 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3927..cbd8495bb6 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
     // Using a loop to handle multiple DOIs
     // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
     // Removing ` ` since the manifest.doi is a string and not a proper list
-    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
         temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 5784a33f2f..07ff7afdd9 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -169,7 +169,7 @@ nextflow_workflow {
             params {
                 monochrome_logs = true
                 test_data       = ''
-                outdir          = 1
+                outdir          = true
             }
             workflow {
                 """

From 0afb9fc98a03c71e3d31c313152a541b38f85146 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 15:59:06 +0200
Subject: [PATCH 21/51] update nf-core/utils_nfcore_pipeline subworkflow

---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 1bb6c3ab13..5f411e2f0a 100644
--- a/modules.json
+++ b/modules.json
@@ -525,7 +525,7 @@
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "1f19c093c86ae49d1899e234d4aa4d56c57be780",
+                        "git_sha": "e6c055a7bb7551ef18436a8ef410dd0e27393c61",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_annotate_ensemblvep": {

From a87503c815d2b863b348c4101d887108c36a9988 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 4 Oct 2024 16:15:33 +0200
Subject: [PATCH 22/51] update nf-core/utils_nfvalidation_plugin subworkflow

---
 .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 07ff7afdd9..c50b1fb532 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -169,7 +169,7 @@ nextflow_workflow {
             params {
                 monochrome_logs = true
                 test_data       = ''
-                outdir          = true
+                outdir          = false
             }
             workflow {
                 """

From 348fb34f192b9301b76d401cd6bfa2b33d1f1abb Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 7 Oct 2024 10:42:59 +0200
Subject: [PATCH 23/51] 4 shards for pipeline

---
 .github/workflows/ci.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0718a79ce7..fd222efeb9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -37,12 +37,6 @@ jobs:
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
         exclude:
-          - filter: "pipeline"
-            shard: 2
-          - filter: "pipeline"
-            shard: 3
-          - filter: "pipeline"
-            shard: 4
           - filter: "pipeline"
             shard: 5
     steps:

From cba29dd63b42e242d0b671c3cd2a396951f0f8f1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Tue, 8 Oct 2024 12:15:55 +0200
Subject: [PATCH 24/51] no need to exclude pipeline shards anymore

---
 .github/workflows/ci.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 02aa25e70a..ab88b3d992 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,9 +36,6 @@ jobs:
         filter: ["pipeline", "workflow", "process", "function"]
         profile: ["docker"]
         shard: [1, 2, 3, 4, 5]
-        exclude:
-          - filter: "pipeline"
-            shard: 5
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

From 44d8f3b1eb467fed75d9f81ee0cbf21ea3a7e9b0 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 11 Oct 2024 09:09:57 +0200
Subject: [PATCH 25/51] remove filter process for now

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1ea73a9129..9de59c2d93 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,8 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        filter: ["process", "workflow", "function", "pipeline"]
+        filter: ["workflow", "function", "pipeline"]
+        # filter: ["process", "workflow", "function", "pipeline"]
         profile: ["conda", "docker", "singularity"]
         shard: [1, 2, 3, 4, 5]
         isMaster:

From 4ba50b2403195f0bc8cbad8ba00145bea5a37fe8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 11 Oct 2024 09:16:33 +0200
Subject: [PATCH 26/51] bump minimum NXF_VER

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index df63fce6f8..978db90c48 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -53,7 +53,7 @@ jobs:
         TEST_DATA_BASE:
           - "test-datasets/data"
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
         exclude:
           - tags: "sentieon/bwamem"

From f4702274cbfa7e3c61869899914f6afa9e001921 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 11 Oct 2024 09:26:08 +0200
Subject: [PATCH 27/51] no status is 0

---
 tests/csv/3.0/mapped_joint_bam.csv | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/csv/3.0/mapped_joint_bam.csv b/tests/csv/3.0/mapped_joint_bam.csv
index 689393be00..1dc3920b1e 100644
--- a/tests/csv/3.0/mapped_joint_bam.csv
+++ b/tests/csv/3.0/mapped_joint_bam.csv
@@ -1,3 +1,3 @@
-patient,sample,bam,bai
-testN,testN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai
-testT,testT,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai
+patient,status,sample,bam,bai
+testN,0,testN,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai
+testT,0,testT,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai

From 038c2ecc7055effdafe0250424cd5197b55f0a3a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:06:10 +0200
Subject: [PATCH 28/51] print tests run

---
 .github/workflows/ci.yml | 33 +++++++++++++++++++++++----------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f171fd1011..47330e6795 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -116,24 +116,37 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
+      - name: "Print tests to run"
         run: |
           nf-test test \
               --ci \
-              --debug \
-              --verbose \
+              --dryrun \
               --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
               --shard ${{ matrix.shard }}/5 \
               --changed-since HEAD^ \
               --follow-dependencies \
               --profile "+${{ matrix.profile }}" \
-              --filter ${{ matrix.filter }}
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v4
-        if: success() || failure() # always run even if the previous step fails
-        with:
-          report_paths: "TEST-*.xml"
+              --filter ${{ matrix.filter }} \
+              | grep PASSED | cut -d "'" -f 2 | sort -u
+
+      # - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
+      #   run: |
+      #     nf-test test \
+      #         --ci \
+      #         --debug \
+      #         --verbose \
+      #         --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+      #         --shard ${{ matrix.shard }}/5 \
+      #         --changed-since HEAD^ \
+      #         --follow-dependencies \
+      #         --profile "+${{ matrix.profile }}" \
+      #         --filter ${{ matrix.filter }}
+
+      # - name: Publish Test Report
+      #   uses: mikepenz/action-junit-report@v4
+      #   if: success() || failure() # always run even if the previous step fails
+      #   with:
+      #     report_paths: "TEST-*.xml"
 
       - name: Clean up
         if: always()

From b182313fcd6be0e1cedb0b6e0a69b88358aa5a8d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:09:05 +0200
Subject: [PATCH 29/51] Typo

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 47330e6795..50d48250f5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -120,7 +120,7 @@ jobs:
         run: |
           nf-test test \
               --ci \
-              --dryrun \
+              --dryRun \
               --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
               --shard ${{ matrix.shard }}/5 \
               --changed-since HEAD^ \

From 5500193bc61676959fe5bf86998d2137fedc5b2c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:12:53 +0200
Subject: [PATCH 30/51] echo the results

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 50d48250f5..1d58d527a6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -118,7 +118,7 @@ jobs:
 
       - name: "Print tests to run"
         run: |
-          nf-test test \
+          echo $(nf-test test \
               --ci \
               --dryRun \
               --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
@@ -127,7 +127,7 @@ jobs:
               --follow-dependencies \
               --profile "+${{ matrix.profile }}" \
               --filter ${{ matrix.filter }} \
-              | grep PASSED | cut -d "'" -f 2 | sort -u
+              | grep PASSED | cut -d "'" -f 2 | sort -u)
 
       # - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
       #   run: |

From 6beaaceade4e97da5cffbf6c19089446e48613df Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:20:29 +0200
Subject: [PATCH 31/51] print to GITHUB_OUTPUT

---
 .github/workflows/ci.yml | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1d58d527a6..350a4db5dc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -117,17 +117,18 @@ jobs:
         uses: jlumbroso/free-disk-space@v1.3.1
 
       - name: "Print tests to run"
+        id: print-test
         run: |
-          echo $(nf-test test \
-              --ci \
-              --dryRun \
-              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
-              --shard ${{ matrix.shard }}/5 \
-              --changed-since HEAD^ \
-              --follow-dependencies \
-              --profile "+${{ matrix.profile }}" \
-              --filter ${{ matrix.filter }} \
-              | grep PASSED | cut -d "'" -f 2 | sort -u)
+          nf-test test \
+            --ci \
+            --dryRun \
+            --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+            --shard ${{ matrix.shard }}/5 \
+            --changed-since HEAD^ \
+            --follow-dependencies \
+            --profile "+${{ matrix.profile }}" \
+            --filter ${{ matrix.filter }} \
+            | grep PASSED | cut -d "'" -f 2 | sort -u >> $GITHUB_OUTPUT
 
       # - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
       #   run: |

From d1f531a792c2095ea6e81c281699f1b5e7ac4698 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:27:33 +0200
Subject: [PATCH 32/51] print to GITHUB_SUMMARY

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 350a4db5dc..0d2ddf3e26 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -116,9 +116,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      - name: "Print tests to run"
-        id: print-test
+      - id: print-test
         run: |
+          echo "### Test summary :rocket:" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \
             --dryRun \
@@ -128,7 +128,7 @@ jobs:
             --follow-dependencies \
             --profile "+${{ matrix.profile }}" \
             --filter ${{ matrix.filter }} \
-            | grep PASSED | cut -d "'" -f 2 | sort -u >> $GITHUB_OUTPUT
+            | grep PASSED | cut -d "'" -f 2 | sort -u >> $GITHUB_STEP_SUMMARY
 
       # - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
       #   run: |

From 5c926086975044281b62d535e220156a6b582583 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:38:27 +0200
Subject: [PATCH 33/51] Better summary

---
 .github/workflows/ci.yml | 54 +++++++++++++++++++++++++---------------
 1 file changed, 34 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0d2ddf3e26..af8bf4193d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -116,9 +116,11 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      - id: print-test
+      - name: Start summary
+        id: print-test
         run: |
-          echo "### Test summary :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "### nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "This shard contains the following tests:" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \
             --dryRun \
@@ -130,24 +132,36 @@ jobs:
             --filter ${{ matrix.filter }} \
             | grep PASSED | cut -d "'" -f 2 | sort -u >> $GITHUB_STEP_SUMMARY
 
-      # - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
-      #   run: |
-      #     nf-test test \
-      #         --ci \
-      #         --debug \
-      #         --verbose \
-      #         --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
-      #         --shard ${{ matrix.shard }}/5 \
-      #         --changed-since HEAD^ \
-      #         --follow-dependencies \
-      #         --profile "+${{ matrix.profile }}" \
-      #         --filter ${{ matrix.filter }}
-
-      # - name: Publish Test Report
-      #   uses: mikepenz/action-junit-report@v4
-      #   if: success() || failure() # always run even if the previous step fails
-      #   with:
-      #     report_paths: "TEST-*.xml"
+      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
+        run: |
+          nf-test test \
+              --ci \
+              --debug \
+              --verbose \
+              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+              --shard ${{ matrix.shard }}/5 \
+              --changed-since HEAD^ \
+              --follow-dependencies \
+              --profile "+${{ matrix.profile }}" \
+              --filter ${{ matrix.filter }}
+
+      - name: Print success in summary
+        if: success()
+        run: |
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "All tests successfull :rocket:" >> $GITHUB_STEP_SUMMARY
+
+      - name: Print failure in summary
+        if: failure()
+        run: |
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "Some tests failed :sadcold_sweat:" >> $GITHUB_STEP_SUMMARY
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: "TEST-*.xml"
 
       - name: Clean up
         if: always()

From 5b4827c431443e41c186952f8fce6bc8849c3698 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 13:53:17 +0200
Subject: [PATCH 34/51] Better summary

---
 .github/workflows/ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index af8bf4193d..db68dbc06c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -120,7 +120,10 @@ jobs:
         id: print-test
         run: |
           echo "### nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
-          echo "This shard contains the following tests:" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "This ${{ matrix.filter }} shard was run on ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | " >> $GITHUB_STEP_SUMMARY
+          echo "This shard contains the following test(s):" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \
             --dryRun \
@@ -149,13 +152,13 @@ jobs:
         if: success()
         run: |
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "All tests successfull :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "All test(s) successfull :rocket:" >> $GITHUB_STEP_SUMMARY
 
       - name: Print failure in summary
         if: failure()
         run: |
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "Some tests failed :sadcold_sweat:" >> $GITHUB_STEP_SUMMARY
+          echo "Some test(s) failed :sadcold_sweat:" >> $GITHUB_STEP_SUMMARY
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v4

From 8d876af9a88fdff474b33fc792b581f497ec3384 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 14:02:47 +0200
Subject: [PATCH 35/51] Better summary

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index db68dbc06c..fecb3cb05d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -121,7 +121,7 @@ jobs:
         run: |
           echo "### nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "This ${{ matrix.filter }} shard was run on ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | " >> $GITHUB_STEP_SUMMARY
+          echo "This ${{ matrix.filter }} shard was run on ${{ matrix.profile }} | ${{ matrix.NXF_VER }}" >> $GITHUB_STEP_SUMMARY
           echo "This shard contains the following test(s):" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           nf-test test \
@@ -133,7 +133,7 @@ jobs:
             --follow-dependencies \
             --profile "+${{ matrix.profile }}" \
             --filter ${{ matrix.filter }} \
-            | grep PASSED | cut -d "'" -f 2 | sort -u >> $GITHUB_STEP_SUMMARY
+            | grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY
 
       - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
         run: |

From e03627e9f2d83e7a824e468ab677152e279e6507 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 14:56:58 +0200
Subject: [PATCH 36/51] update to python v5

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fecb3cb05d..8a34a87843 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,7 +52,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
         with:
           python-version: "3.11"
           architecture: "x64"

From 1370581bb38465e7716735adcd566339b60e35b9 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 15:12:38 +0200
Subject: [PATCH 37/51] nicer summary

---
 .github/workflows/ci.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8a34a87843..de3f46e9a1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -119,10 +119,9 @@ jobs:
       - name: Start summary
         id: print-test
         run: |
-          echo "### nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "This ${{ matrix.filter }} shard was run on ${{ matrix.profile }} | ${{ matrix.NXF_VER }}" >> $GITHUB_STEP_SUMMARY
-          echo "This shard contains the following test(s):" >> $GITHUB_STEP_SUMMARY
+          echo "This `${{ matrix.filter }}` shard was run on `${{ matrix.profile }}` | `NXF_VER=${{ matrix.NXF_VER }}`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \
@@ -152,7 +151,7 @@ jobs:
         if: success()
         run: |
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "All test(s) successfull :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "All test(s) successfull :party:" >> $GITHUB_STEP_SUMMARY
 
       - name: Print failure in summary
         if: failure()

From 9815858c3ecf4b761f18e52ba25c785038cd7d85 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 16:04:49 +0200
Subject: [PATCH 38/51] escape single quote

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index de3f46e9a1..8cf523dd22 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -121,7 +121,7 @@ jobs:
         run: |
           echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "This `${{ matrix.filter }}` shard was run on `${{ matrix.profile }}` | `NXF_VER=${{ matrix.NXF_VER }}`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
+          echo "This \`${{ matrix.filter }}\` shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \

From 105821fcb4dfb19f017fd5b408986384c04d703d Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 16:13:29 +0200
Subject: [PATCH 39/51] polish

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8cf523dd22..4cd6ef7d2b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -121,7 +121,7 @@ jobs:
         run: |
           echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "This \`${{ matrix.filter }}\` shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
+          echo "This \`${{ matrix.filter }}\` ${{ matrix.shard }}/5 shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           nf-test test \
             --ci \
@@ -151,13 +151,13 @@ jobs:
         if: success()
         run: |
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "All test(s) successfull :party:" >> $GITHUB_STEP_SUMMARY
+          echo "All test(s) successfull :tada:" >> $GITHUB_STEP_SUMMARY
 
       - name: Print failure in summary
         if: failure()
         run: |
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "Some test(s) failed :sadcold_sweat:" >> $GITHUB_STEP_SUMMARY
+          echo "Some test(s) failed :cold_sweat:" >> $GITHUB_STEP_SUMMARY
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v4

From 2fab5f92941516f0c6221908680b0d5d3d6cdac2 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 16:34:43 +0200
Subject: [PATCH 40/51] try concatenate reports

---
 .github/workflows/ci.yml | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4cd6ef7d2b..78d574f07e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,8 +33,9 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
-        filter: ["workflow", "function", "pipeline"]
+          # - "latest-everything"
+        filter: ["workflow"]
+        # filter: ["workflow", "function", "pipeline"]
         # filter: ["process", "workflow", "function", "pipeline"]
         profile: ["conda", "docker", "singularity"]
         shard: [1, 2, 3, 4, 5]
@@ -161,11 +162,34 @@ jobs:
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v4
-        if: success() || failure() # always run even if the previous step fails
+        if: always() # always run even if the previous step fails
         with:
           report_paths: "TEST-*.xml"
 
+      - name: Upload Test Report
+        uses: actions/upload-artifact@v3
+        if: always() # always run even if the previous step fails
+        with:
+          name: junit-test-results
+          path: "**/build/test-results/test/TEST-*.xml"
+          retention-days: 1
+
       - name: Clean up
         if: always()
         run: |
           sudo rm -rf /home/ubuntu/tests/
+
+  checks:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download Test Report
+        uses: dawidd6/action-download-artifact@v2
+        with:
+          name: junit-test-results
+          workflow: ${{ github.event.workflow.id }}
+          run_id: ${{ github.event.workflow_run.id }}
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        with:
+          commit: ${{github.event.workflow_run.head_sha}}
+          report_paths: "**/build/test-results/test/TEST-*.xml"

From 2b6b408154abccc96ee0449720573045a106d815 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 16:56:13 +0200
Subject: [PATCH 41/51] fix path

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 78d574f07e..a2c67bfec0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -171,7 +171,7 @@ jobs:
         if: always() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "**/build/test-results/test/TEST-*.xml"
+          path: "TEST-*.xml"
           retention-days: 1
 
       - name: Clean up
@@ -188,8 +188,9 @@ jobs:
           name: junit-test-results
           workflow: ${{ github.event.workflow.id }}
           run_id: ${{ github.event.workflow_run.id }}
+
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
         with:
           commit: ${{github.event.workflow_run.head_sha}}
-          report_paths: "**/build/test-results/test/TEST-*.xml"
+          report_paths: "TEST-*.xml"

From 36cedb3cf68b528ba860f54e06515cb9258611d8 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 17:05:55 +0200
Subject: [PATCH 42/51] add needs

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a2c67bfec0..c22c74a593 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -181,6 +181,7 @@ jobs:
 
   checks:
     runs-on: ubuntu-latest
+    needs: [test]
     steps:
       - name: Download Test Report
         uses: dawidd6/action-download-artifact@v2

From a1cb1c4b8b5b04fb5c8a3bfcf6cdc9c5d2531d23 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 17:17:10 +0200
Subject: [PATCH 43/51] update actions

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c22c74a593..18f73ddedf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -184,14 +184,14 @@ jobs:
     needs: [test]
     steps:
       - name: Download Test Report
-        uses: dawidd6/action-download-artifact@v2
+        uses: dawidd6/action-download-artifact@v6
         with:
           name: junit-test-results
           workflow: ${{ github.event.workflow.id }}
           run_id: ${{ github.event.workflow_run.id }}
 
       - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
+        uses: mikepenz/action-junit-report@v4
         with:
           commit: ${{github.event.workflow_run.head_sha}}
           report_paths: "TEST-*.xml"

From bfb3a3805fa05881ec38e04f89557d3d98107c2c Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 17:24:42 +0200
Subject: [PATCH 44/51] update action

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 18f73ddedf..6a647e06e1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -167,7 +167,7 @@ jobs:
           report_paths: "TEST-*.xml"
 
       - name: Upload Test Report
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: always() # always run even if the previous step fails
         with:
           name: junit-test-results

From 2d094ee8e1badb0ca5be8a117c99429f3df0e0e3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 17:35:39 +0200
Subject: [PATCH 45/51] update path

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6a647e06e1..015be54294 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -171,7 +171,7 @@ jobs:
         if: always() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "TEST-*.xml"
+          path: "**/build/test-results/test/TEST-*.xml"
           retention-days: 1
 
       - name: Clean up
@@ -194,4 +194,4 @@ jobs:
         uses: mikepenz/action-junit-report@v4
         with:
           commit: ${{github.event.workflow_run.head_sha}}
-          report_paths: "TEST-*.xml"
+          report_paths: "**/build/test-results/test/TEST-*.xml"

From 0ddea42180bf7898e43d729916c1854f216c0d3a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 18:27:08 +0200
Subject: [PATCH 46/51] update path

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 015be54294..381d8d97d9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -162,20 +162,20 @@ jobs:
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v4
-        if: always() # always run even if the previous step fails
+        if: success() || failure() # always run even if the previous step fails
         with:
           report_paths: "TEST-*.xml"
 
       - name: Upload Test Report
         uses: actions/upload-artifact@v4
-        if: always() # always run even if the previous step fails
+        if: success() || failure() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "**/build/test-results/test/TEST-*.xml"
+          path: "TEST-*.xml"
           retention-days: 1
 
       - name: Clean up
-        if: always()
+        if: success() || failure()
         run: |
           sudo rm -rf /home/ubuntu/tests/
 

From 2de9bf18025d6cd3c30609bfc0c2f6dd8d683cb1 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 18:32:08 +0200
Subject: [PATCH 47/51] update path

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 381d8d97d9..fe0a9e8b31 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -164,14 +164,14 @@ jobs:
         uses: mikepenz/action-junit-report@v4
         if: success() || failure() # always run even if the previous step fails
         with:
-          report_paths: "TEST-*.xml"
+          report_paths: "TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
 
       - name: Upload Test Report
         uses: actions/upload-artifact@v4
         if: success() || failure() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "TEST-*.xml"
+          path: "TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
           retention-days: 1
 
       - name: Clean up

From 67269a9d9b55dd0c115db1f869a69f9c5b21f66e Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 18:37:54 +0200
Subject: [PATCH 48/51] update path

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fe0a9e8b31..492810538b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -164,14 +164,14 @@ jobs:
         uses: mikepenz/action-junit-report@v4
         if: success() || failure() # always run even if the previous step fails
         with:
-          report_paths: "TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
+          report_paths: "TEST-report_${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
 
       - name: Upload Test Report
         uses: actions/upload-artifact@v4
         if: success() || failure() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
+          path: "TEST-report_${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
           retention-days: 1
 
       - name: Clean up

From 1c06bab3c62ad822fbfc426e3cffa2f9f50e5a24 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 24 Oct 2024 18:43:37 +0200
Subject: [PATCH 49/51] revert to v3

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 492810538b..20e35e19fc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -164,14 +164,14 @@ jobs:
         uses: mikepenz/action-junit-report@v4
         if: success() || failure() # always run even if the previous step fails
         with:
-          report_paths: "TEST-report_${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
+          report_paths: "TEST-*.xml"
 
       - name: Upload Test Report
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v3
         if: success() || failure() # always run even if the previous step fails
         with:
           name: junit-test-results
-          path: "TEST-report_${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml"
+          path: "TEST-*.xml"
           retention-days: 1
 
       - name: Clean up
@@ -194,4 +194,4 @@ jobs:
         uses: mikepenz/action-junit-report@v4
         with:
           commit: ${{github.event.workflow_run.head_sha}}
-          report_paths: "**/build/test-results/test/TEST-*.xml"
+          report_paths: "TEST-*.xml"

From 04dca873963f8912b586e2b25e709a0b9aecdc63 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 25 Oct 2024 13:46:19 +0200
Subject: [PATCH 50/51] revert to a working state

---
 .github/workflows/ci.yml | 30 ++----------------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 20e35e19fc..8ed6cebe7e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,9 +33,8 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          # - "latest-everything"
-        filter: ["workflow"]
-        # filter: ["workflow", "function", "pipeline"]
+          - "latest-everything"
+        filter: ["workflow", "function", "pipeline"]
         # filter: ["process", "workflow", "function", "pipeline"]
         profile: ["conda", "docker", "singularity"]
         shard: [1, 2, 3, 4, 5]
@@ -166,32 +165,7 @@ jobs:
         with:
           report_paths: "TEST-*.xml"
 
-      - name: Upload Test Report
-        uses: actions/upload-artifact@v3
-        if: success() || failure() # always run even if the previous step fails
-        with:
-          name: junit-test-results
-          path: "TEST-*.xml"
-          retention-days: 1
-
       - name: Clean up
         if: success() || failure()
         run: |
           sudo rm -rf /home/ubuntu/tests/
-
-  checks:
-    runs-on: ubuntu-latest
-    needs: [test]
-    steps:
-      - name: Download Test Report
-        uses: dawidd6/action-download-artifact@v6
-        with:
-          name: junit-test-results
-          workflow: ${{ github.event.workflow.id }}
-          run_id: ${{ github.event.workflow_run.id }}
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v4
-        with:
-          commit: ${{github.event.workflow_run.head_sha}}
-          report_paths: "TEST-*.xml"

From f3b96aa5925643f7bf01856d17856cd180761485 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Mon, 28 Oct 2024 11:11:19 +0100
Subject: [PATCH 51/51] Apply suggestions from code review

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ed6cebe7e..7249747614 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,7 +33,7 @@ jobs:
       matrix:
         NXF_VER:
           - "24.04.2"
-          - "latest-everything"
+          # - "latest-everything"
         filter: ["workflow", "function", "pipeline"]
         # filter: ["process", "workflow", "function", "pipeline"]
         profile: ["conda", "docker", "singularity"]