diff --git a/.github/workflows/code-linting-develop.yml b/.github/workflows/code-linting-develop.yml
new file mode 100644
index 000000000000..df3365dfa011
--- /dev/null
+++ b/.github/workflows/code-linting-develop.yml
@@ -0,0 +1,38 @@
+name: Code Linting Develop
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Install NodeJS
+        uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  EditorConfig:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v2
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: Run ECLint check
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
diff --git a/.github/workflows/nf-core-linting-develop.yml b/.github/workflows/nf-core-linting-develop.yml
new file mode 100644
index 000000000000..c12059ab168d
--- /dev/null
+++ b/.github/workflows/nf-core-linting-develop.yml
@@ -0,0 +1,80 @@
+name: nf-core linting develop
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  lint:
+    runs-on: ubuntu-20.04
+    name: ${{ matrix.tags }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+      - name: Install nf-core tools
+        run: python -m pip install nf-core
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint ${{ matrix.tags }}
+        # HACK
+        if: startsWith( matrix.tags, 'subworkflow' ) != true
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}
diff --git a/.github/workflows/nf-test-develop.yml b/.github/workflows/nf-test-develop.yml
new file mode 100644
index 000000000000..d139dc6a07e1
--- /dev/null
+++ b/.github/workflows/nf-test-develop.yml
@@ -0,0 +1,177 @@
+name: nf-test-develop
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/nftest_modules.yml"
+
+  test:
+    runs-on: ubuntu-20.04
+
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: sentieon/bwaindex
+          - profile: "conda"
+            tags: sentieon/bwamem
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+    env:
+      NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
diff --git a/.github/workflows/pytest-workflow-develop.yml b/.github/workflows/pytest-workflow-develop.yml
new file mode 100644
index 000000000000..ab278ab3402b
--- /dev/null
+++ b/.github/workflows/pytest-workflow-develop.yml
@@ -0,0 +1,229 @@
+name: Pytest-workflow-develop
+on:
+  pull_request:
+    branches: [develop]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_modules.yml"
+
+  test:
+    runs-on: ubuntu-20.04
+
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
+        profile: ["docker", "singularity", "conda"]
+        exclude:
+          - profile: "conda"
+            tags: annotsv
+          - profile: "conda"
+            tags: cellpose
+          - profile: "conda"
+            tags: mcquant
+          - profile: "conda"
+            tags: bases2fastq
+          - profile: "conda"
+            tags: backsub
+          - profile: "conda"
+            tags: basicpy
+          - profile: "conda"
+            tags: bcl2fastq
+          - profile: "conda"
+            tags: bclconvert
+          - profile: "conda"
+            tags: cellranger/count
+          - profile: "conda"
+            tags: cellranger/mkfastq
+          - profile: "conda"
+            tags: cellranger/mkgtf
+          - profile: "conda"
+            tags: cellranger/mkref
+          - profile: "conda"
+            tags: cellranger/mkvdjref
+          - profile: "conda"
+            tags: cellranger/multi
+          - profile: "conda"
+            tags: cellranger/vdj
+          - profile: "conda"
+            tags: coreograph
+          - profile: "conda"
+            tags: deepcell/mesmer
+          - profile: "conda"
+            tags: deepvariant
+          - profile: "conda"
+            tags: ensemblvep/vep
+          - profile: "conda"
+            tags: fastk/fastk
+          - profile: "conda"
+            tags: fastk/histex
+          - profile: "conda"
+            tags: fastk/merge
+          - profile: "conda"
+            tags: fcs/fcsadaptor
+          - profile: "conda"
+            tags: fcs/fcsgx
+          - profile: "conda"
+            tags: gatk4/baserecalibratorspark
+          - profile: "conda"
+            tags: gatk4/cnnscorevariants
+          - profile: "conda"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: gatk4/germlinecnvcaller
+          - profile: "conda"
+            tags: gatk4/markduplicatesspark
+          - profile: "conda"
+            tags: gatk4/postprocessgermlinecnvcalls
+          - profile: "conda"
+            tags: genescopefk
+          - profile: "conda"
+            tags: ilastik/multicut
+          - profile: "conda"
+            tags: ilastik/pixelclassification
+          - profile: "conda"
+            tags: imputeme/vcftoprs
+          - profile: "conda"
+            tags: merquryfk/katcomp
+          - profile: "conda"
+            tags: merquryfk/katgc
+          - profile: "conda"
+            tags: merquryfk/merquryfk
+          - profile: "conda"
+            tags: merquryfk/ploidyplot
+          - profile: "conda"
+            tags: mitohifi/findmitoreference
+          - profile: "conda"
+            tags: scimap/mcmicro
+          - tags: "sentieon/*"
+          - profile: "conda"
+            tags: universc
+          - profile: "singularity"
+            tags: universc
+          - profile: "singularity"
+            tags: gatk4/determinegermlinecontigploidy
+          - profile: "conda"
+            tags: subworkflows/bcl_demultiplex
+          - profile: "conda"
+            tags: subworkflows/vcf_annotate_ensemblvep
+          - profile: "conda"
+            tags: islandpath
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow cryptography
+
+      - uses: actions/cache@v3
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get update > /dev/null
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Setting global variables
+        uses: actions/github-script@v6
+        id: parsed
+        with:
+          script: |
+            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
+          result-encoding: string
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 2c2c5fbb7189..44a2c827bd18 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -148,8 +148,6 @@ jobs:
             tags: gatk4/determinegermlinecontigploidy
           - profile: "conda"
             tags: subworkflows/bcl_demultiplex
-          - profile: "conda"
-            tags: subworkflows/vcf_annotate_ensemblvep_snpeff
           - profile: "conda"
             tags: subworkflows/vcf_annotate_ensemblvep
           - profile: "conda"
diff --git a/.github/workflows/sync-action.yml b/.github/workflows/sync-action.yml
new file mode 100644
index 000000000000..c16d4537aad0
--- /dev/null
+++ b/.github/workflows/sync-action.yml
@@ -0,0 +1,24 @@
+name: Sync Fork
+
+on:
+  schedule:
+    - cron: "0 0 * * *" # run once a night at midnight
+  workflow_dispatch: # on button click
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Sync master branch
+        uses: tgymnich/fork-sync@v1.8
+        with:
+          token: ${{ secrets.PERSONAL_TOKEN }}
+          base: master
+          head: master
+      - name: Sync develop branch
+        uses: tgymnich/fork-sync@v1.8
+        with:
+          token: ${{ secrets.PERSONAL_TOKEN }}
+          base: develop
+          head: master
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
index 0a775ebebb27..dbc00e00b16e 100644
--- a/modules/nf-core/bcftools/query/main.nf
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -1,6 +1,6 @@
 process BCFTOOLS_QUERY {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_medium'
 
     conda "bioconda::bcftools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -28,12 +28,12 @@ process BCFTOOLS_QUERY {
     def samples_file =  samples ? "--samples-file ${samples}" : ""
     """
     bcftools query \\
+        --output ${prefix}.txt \\
         $regions_file \\
         $targets_file \\
         $samples_file \\
         $args \\
-        $vcf \\
-        > ${prefix}.txt
+        $vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/mergefastq/main.nf b/modules/nf-core/mergefastq/main.nf
new file mode 100644
index 000000000000..846a4832df69
--- /dev/null
+++ b/modules/nf-core/mergefastq/main.nf
@@ -0,0 +1,37 @@
+process MERGEFASTQ {
+    tag "$meta.id"
+    label 'process_low'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using merge. Please use docker or singularity containers."
+    }
+    container "ghcr.io/mskcc-omics-workflows/merge-gzip:1.6-5ubuntu1.2"
+
+    input:
+    tuple val(meta), path(fastq_1), path(fastq_2)
+
+    output:
+    tuple val(meta), path("*_R*_mrg.fastq.gz")      ,emit: mrg_fq
+    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}"
+    def fastq_filter = fastq_2.name != "null" ? fastq_2 : ""
+
+    """
+    zcat \\
+    ${fastq_1} \\
+    ${fastq_filter} \\
+    | \\
+    gzip > ${meta.sample_name}_L000_R${meta.read}_mrg.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mergefastq: \$(echo \$(gzip --version 2>&1) | sed 's/^.*gzip //; s/Copyright.*\$//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/mergefastq/meta.yml b/modules/nf-core/mergefastq/meta.yml
new file mode 100644
index 000000000000..deb719fce42a
--- /dev/null
+++ b/modules/nf-core/mergefastq/meta.yml
@@ -0,0 +1,49 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "mergefastq"
+description: Merge a pair of raw fastq files from two different lanes (single fastq file is also acceptable)
+keywords:
+  - msk
+  - mergefastq
+  - zcat
+  - gzip
+tools:
+  - "gzip":
+      description: "Files to compress or decompress"
+      homepage: "https://www.gzip.org/"
+      documentation: "https://www.gzip.org/"
+      licence: ""
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', sample_name:'Sample-T', read:'1' ]
+  - fastq_1:
+      type: file
+      description: fastq file from Lane 1
+      pattern: "*_{L001_,}R*_001.fastq.gz"
+  - fastq_2: # Optional if there is only one fastq file
+      type: file
+      description: fastq file from Lane 2
+      pattern: "*_L002_R*_001.fastq.gz" # OR null
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', sample_name:'Sample-T', read:'1' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - mrg_fq:
+      type: file
+      description: Merge fastq file
+      pattern: "*_R*_mrg.fastq.gz"
+
+authors:
+  - "@huyu335"
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index d6c5a760f3da..fe8160bae4cd 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -11,8 +11,7 @@ process TABIX_BGZIPTABIX {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.gz"), path("*.tbi"), optional: true, emit: gz_tbi
-    tuple val(meta), path("*.gz"), path("*.csi"), optional: true, emit: gz_csi
+    tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
     path  "versions.yml" ,                        emit: versions
 
     when:
@@ -37,7 +36,6 @@ process TABIX_BGZIPTABIX {
     """
     touch ${prefix}.${input.getExtension()}.gz
     touch ${prefix}.${input.getExtension()}.gz.tbi
-    touch ${prefix}.${input.getExtension()}.gz.csi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
index 2761e27183bb..49c032894157 100644
--- a/modules/nf-core/tabix/bgziptabix/meta.yml
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -37,14 +37,9 @@ output:
       type: file
       description: tabix index file
       pattern: "*.{gz.tbi}"
-  - csi:
-      type: file
-      description: tabix alternate index file
-      pattern: "*.{gz.csi}"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@maxulysse"
-  - "@DLBPointon"
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
deleted file mode 100644
index 91cace4d1d9f..000000000000
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ /dev/null
@@ -1,191 +0,0 @@
-//
-// Run VEP and/or SNPEFF to annotate VCF files
-//
-
-include { ENSEMBLVEP_VEP         } from '../../../modules/nf-core/ensemblvep/vep/main'
-include { SNPEFF_SNPEFF          } from '../../../modules/nf-core/snpeff/snpeff/main'
-include { TABIX_TABIX            } from '../../../modules/nf-core/tabix/tabix/main'
-include { BCFTOOLS_PLUGINSCATTER } from '../../../modules/nf-core/bcftools/pluginscatter/main'
-include { BCFTOOLS_CONCAT        } from '../../../modules/nf-core/bcftools/concat/main'
-include { BCFTOOLS_SORT          } from '../../../modules/nf-core/bcftools/sort/main'
-
-workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
-    take:
-    ch_vcf                      // channel: [ val(meta), path(vcf), path(tbi), [path(file1), path(file2)...] ]
-    ch_fasta                    // channel: [ val(meta2), path(fasta) ] (optional)
-    val_vep_genome              //   value: genome to use
-    val_vep_species             //   value: species to use
-    val_vep_cache_version       //   value: cache version to use
-    ch_vep_cache                // channel: [ path(cache) ] (optional)
-    ch_vep_extra_files          // channel: [ path(file1), path(file2)... ] (optional)
-    val_snpeff_db               //   value: the db version to use for snpEff
-    ch_snpeff_cache             // channel: [ path(cache) ] (optional)
-    val_tools_to_use            //   value: a list of tools to use options are: ["ensemblvep", "snpeff"]
-    val_sites_per_chunk         //   value: the amount of variants per scattered VCF
-
-    main:
-    ch_versions = Channel.empty()
-
-    // Check if val_sites_per_chunk is set and scatter if it is
-    if(val_sites_per_chunk) {
-        //
-        // Prepare the input VCF channel for scattering (split VCFs from custom files)
-        //
-
-        ch_input = ch_vcf
-            .multiMap { meta, vcf, tbi, custom_files ->
-                vcf:    [ meta, vcf, tbi ]
-                custom: [ meta, custom_files ]
-            }
-
-        //
-        // Scatter the input VCFs into multiple VCFs. These VCFs contain the amount of variants
-        // specified by `val_sites_per_chunk`. The lower this value is, the more files will be created
-        //
-
-        BCFTOOLS_PLUGINSCATTER(
-            ch_input.vcf,
-            val_sites_per_chunk,
-            [],
-            [],
-            [],
-            []
-        )
-        ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSCATTER.out.versions.first())
-
-        //
-        // Run the annotation with EnsemblVEP
-        //
-
-        ch_scatter = BCFTOOLS_PLUGINSCATTER.out.scatter
-            .map { meta, vcfs ->
-                // This checks if multiple files were created using the scatter process
-                // If multiple files are created, a list will be made as output of the process
-                // So if the output isn't a list, there is always one file and if there is a list,
-                // the amount of files in the list gets counted by .size()
-                is_list = vcfs instanceof ArrayList
-                count = is_list ? vcfs.size() : 1
-                [ meta, is_list ? vcfs : [vcfs], count ]
-                // Channel containing the list of VCFs and the size of this list
-            }
-            .transpose(by:1) // Transpose on the VCFs => Creates an entry for each VCF in the list
-            .combine(ch_input.custom, by: 0) // Re-add the sample specific custom files
-            .multiMap { meta, vcf, count, custom_files ->
-                // Define the new ID. The `_annotated` is to disambiguate the VEP output with its input
-                new_id = "${meta.id}${vcf.name.replace(meta.id,"").tokenize(".")[0]}_annotated" as String
-                new_meta = meta + [id:new_id]
-
-                // Create channels: one with the VEP input and one with the original ID and count of scattered VCFs
-                input:  [ new_meta, vcf, custom_files ]
-                count:  [ new_meta, meta.id, count ]
-            }
-
-        ch_vep_input = ch_scatter.input
-    } else {
-        // Use the normal input when no scattering has to be performed
-        ch_vep_input = ch_vcf.map { meta, vcf, tbi, files -> [ meta, vcf, files ] }
-    }
-
-    // Annotate with ensemblvep if it's part of the requested tools
-    if("ensemblvep" in val_tools_to_use){
-        ENSEMBLVEP_VEP(
-            ch_vep_input,
-            val_vep_genome,
-            val_vep_species,
-            val_vep_cache_version,
-            ch_vep_cache,
-            ch_fasta,
-            ch_vep_extra_files
-        )
-        ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions.first())
-
-        ch_vep_output  = ENSEMBLVEP_VEP.out.vcf
-        ch_vep_reports = ENSEMBLVEP_VEP.out.report
-    } else {
-        ch_vep_output  = ch_vep_input.map { meta, vcf, files -> [ meta, vcf ] }
-        ch_vep_reports = Channel.empty()
-    }
-
-    // Annotate with snpeff if it's part of the requested tools
-    if("snpeff" in val_tools_to_use){
-        SNPEFF_SNPEFF(
-            ch_vep_output,
-            val_snpeff_db,
-            ch_snpeff_cache
-        )
-        ch_versions = ch_versions.mix(SNPEFF_SNPEFF.out.versions.first())
-
-        ch_snpeff_output  = SNPEFF_SNPEFF.out.vcf
-        ch_snpeff_reports = SNPEFF_SNPEFF.out.report
-        ch_snpeff_html    = SNPEFF_SNPEFF.out.summary_html
-        ch_snpeff_genes   = SNPEFF_SNPEFF.out.genes_txt
-    } else {
-        ch_snpeff_output  = ch_vep_output
-        ch_snpeff_reports = Channel.empty()
-        ch_snpeff_html    = Channel.empty()
-        ch_snpeff_genes   = Channel.empty()
-    }
-
-    // Gather the files back together if they were scattered
-    if(val_sites_per_chunk) {
-        //
-        // Concatenate the VCFs back together with bcftools concat
-        //
-
-        ch_concat_input = ch_snpeff_output
-            .join(ch_scatter.count, failOnDuplicate:true, failOnMismatch:true)
-            .map { meta, vcf, id, count ->
-                new_meta = meta + [id:id]
-                [ groupKey(new_meta, count), vcf ]
-            }
-            .groupTuple() // Group the VCFs which need to be concatenated
-            .map { it + [[]] }
-
-        BCFTOOLS_CONCAT(
-            ch_concat_input
-        )
-        ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions.first())
-
-        //
-        // Sort the concatenate output (bcftools concat is unable to do this on its own)
-        //
-
-        BCFTOOLS_SORT(
-            BCFTOOLS_CONCAT.out.vcf
-        )
-        ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions.first())
-
-        ch_ready_vcfs = BCFTOOLS_SORT.out.vcf
-    } else {
-        ch_ready_vcfs = ch_snpeff_output
-    }
-
-    //
-    // Index the resulting bgzipped VCFs
-    //
-
-    ch_tabix_input = ch_ready_vcfs
-        .branch { meta, vcf ->
-            // Split the bgzipped VCFs from the unzipped VCFs (only bgzipped VCFs should be indexed)
-            bgzip: vcf.extension == "gz"
-            unzip: true
-                return [ meta, vcf, [] ]
-        }
-
-    TABIX_TABIX(
-        ch_tabix_input.bgzip
-    )
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
-
-    ch_vcf_tbi = ch_tabix_input.bgzip
-        .join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true)
-        .mix(ch_tabix_input.unzip)
-
-    emit:
-    vcf_tbi         = ch_vcf_tbi        // channel: [ val(meta), path(vcf), path(tbi) ]
-    vep_reports     = ch_vep_reports    // channel: [ path(html) ]
-    snpeff_reports  = ch_snpeff_reports // channel: [ path(csv) ]
-    snpeff_html     = ch_snpeff_html    // channel: [ path(html) ]
-    snpeff_genes    = ch_snpeff_genes   // channel: [ path(genes) ]
-    versions        = ch_versions       // channel: [ versions.yml ]
-}
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml
deleted file mode 100644
index 211144330be6..000000000000
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml
+++ /dev/null
@@ -1,73 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: vcf_annotate_ensemblvep_snpeff
-description: |
-  Perform annotation with ensemblvep and/or snpeff and bgzip + tabix index the resulting VCF file. This subworkflow uses the scatter-gather method to run VEP/snpEff in parallel to increase throughput. The input VCF is split into multiple smaller VCFs of fixed size, which are annotated separately and concatenated back together to a single output file per sample. Only VCF/BCF outputs are currently supported.
-keywords:
-  - vcf
-  - annotation
-  - ensemblvep
-  - snpeff
-modules:
-  - ensemblvep/vep
-  - snpeff/snpeff
-  - tabix/tabix
-  - bcftools/pluginscatter
-  - bcftools/concat
-input:
-  - ch_vcf:
-      description: |
-        vcf file to annotate
-        Structure: [ val(meta), path(vcf), path(tbi) ]
-  - ch_fasta:
-      description: |
-        Reference genome fasta file (optional)
-        Structure: [ val(meta2), path(fasta) ]
-  - val_vep_genome:
-      type: string
-      description: genome to use for ensemblvep
-  - val_vep_species:
-      type: string
-      description: species to use for ensemblvep
-  - val_vep_cache_version:
-      type: integer
-      description: cache version to use for ensemblvep
-  - ch_vep_cache:
-      description: |
-        the root cache folder for ensemblvep (optional)
-        Structure: [ path(cache) ]
-  - ch_vep_extra_files:
-      description: |
-        any extra files needed by plugins for ensemblvep (optional)
-        Structure: [ path(file1), path(file2)... ]
-  - val_snpeff_db:
-      type: string
-      description: database to use for snpeff
-  - ch_snpeff_cache:
-      description: |
-        the root cache folder for snpeff (optional)
-        Structure: [ path(cache) ]
-  - val_tools_to_use:
-      type: list
-      description: The tools to use. Options => '["ensemblvep", "snpeff"]'
-  - val_sites_per_chunk:
-      type: integer
-      description: |
-        The amount of variants per scattered VCF.
-        Set this value to `null`, `[]` or `false` to disable scattering.
-output:
-  - vcf_tbi:
-      description: |
-        Compressed vcf file + tabix index
-        Structure: [ val(meta), path(vcf), path(tbi) ]
-  - reports:
-      type: file
-      description: html reports
-      pattern: "*.html"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@maxulysse"
-  - "@matthdsm"
-  - "@nvnieuwk"
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index b6db38865d95..504ef74ee3a6 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -36,6 +36,7 @@ conda { createTimeout = "120 min" }
 
 // Load test_data.config containing paths to test data
 includeConfig 'test_data.config'
+includeConfig 'test_data_msk.config'
 
 manifest {
     nextflowVersion = '!>=22.10.1'
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index dd96ec96d09f..72e7e637be55 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -2426,6 +2426,10 @@ msisensorpro/scan:
   - modules/nf-core/msisensorpro/scan/**
   - tests/modules/nf-core/msisensorpro/scan/**
 
+mergefastq:
+  - modules/nf-core/mergefastq/**
+  - tests/modules/nf-core/mergefastq/**
+
 mtnucratio:
   - modules/nf-core/mtnucratio/**
   - tests/modules/nf-core/mtnucratio/**
@@ -3648,10 +3652,6 @@ subworkflows/vcf_annotate_ensemblvep:
   - subworkflows/nf-core/vcf_annotate_ensemblvep/**
   - tests/subworkflows/nf-core/vcf_annotate_ensemblvep/**
 
-subworkflows/vcf_annotate_ensemblvep_snpeff:
-  - subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/**
-  - tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/**
-
 subworkflows/vcf_annotate_snpeff:
   - subworkflows/nf-core/vcf_annotate_snpeff/**
   - tests/subworkflows/nf-core/vcf_annotate_snpeff/**
diff --git a/tests/config/test_data_msk.config b/tests/config/test_data_msk.config
new file mode 100644
index 000000000000..58b7b61b7148
--- /dev/null
+++ b/tests/config/test_data_msk.config
@@ -0,0 +1,12 @@
+params {
+    // Base directory for test data
+    test_data_msk_base = "https://raw.githubusercontent.com/mskcc-omics-workflows/test-datasets"
+
+    test_data_msk {
+        'rawfastq' {
+            fastq_1                                            = "${params.test_data_msk_base}/master/raw_fastq/Sample1-T2_L001_R1_001.fastq.gz"
+            fastq_2                                            = "${params.test_data_msk_base}/master/raw_fastq/Sample1-T2_L002_R1_001.fastq.gz"
+            fastq_no_lane                                      = "${params.test_data_msk_base}/master/raw_fastq/Sample1-T2_R2_001.fastq.gz"
+        }
+    }
+}
diff --git a/tests/modules/nf-core/bcftools/query/test.yml b/tests/modules/nf-core/bcftools/query/test.yml
index 7acf1880dbda..829ee630e4d9 100644
--- a/tests/modules/nf-core/bcftools/query/test.yml
+++ b/tests/modules/nf-core/bcftools/query/test.yml
@@ -1,19 +1,17 @@
-- name: bcftools query test_bcftools_query
+- name: bcftools query
   command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
   tags:
     - bcftools
     - bcftools/query
   files:
     - path: output/bcftools/out.txt
-      md5sum: 51d135de052f3bcef50dcd6b74806094
-    - path: output/bcftools/versions.yml
+      md5sum: c32a6d28f185822d8fe1eeb7e42ec155
 
-- name: bcftools query test_bcftools_query_with_optional_files
+- name: bcftools query with optional files
   command: nextflow run ./tests/modules/nf-core/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/query/nextflow.config
   tags:
     - bcftools
     - bcftools/query
   files:
     - path: output/bcftools/out.txt
-      md5sum: 1785d1957ba7206df852d0689b91753f
-    - path: output/bcftools/versions.yml
+      md5sum: 5a87e0865df2f0ab2884fc113ec2a70d
diff --git a/tests/modules/nf-core/mergefastq/main.nf b/tests/modules/nf-core/mergefastq/main.nf
new file mode 100644
index 000000000000..bce237bce79a
--- /dev/null
+++ b/tests/modules/nf-core/mergefastq/main.nf
@@ -0,0 +1,39 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERGEFASTQ } from '../../../../modules/nf-core/mergefastq/main.nf'
+
+//ch_test_data = Channel.fromFilePairs('Sample*_L00{1,2}_R1_001.fastq.gz')
+//    .flatten()
+//    .toList()
+//    .set { ch_pair_data }
+
+// Sample*_R2_001.fastq.gz
+//ch_test_data = Channel.fromPath('Sample*_L00{1,2}_R1_001.fastq.gz', checkIfExists:true)
+ch_test_data = Channel.fromPath([params.test_data_msk['rawfastq']['fastq_1'], params.test_data_msk['rawfastq']['fastq_2']], checkIfExists:true)
+    .toList()
+    .map { fastq -> 
+        def fastq_list = fastq.size == 2 ? fastq : fastq + [file("null")] // For single fastq file
+        fastq_list }
+    .flatten()
+    .toList()
+    .set{ ch_pair_data }
+meta = [ id:'test', sample_name:'', read:'' ] // meta map
+
+workflow test_mergefastq {
+    
+    ch_pair_data
+        .map { fastq_1, fastq_2 ->
+                meta.read = fastq_1.name.split('_')[-2].replace("R", "") // get read name
+                meta.sample_name = fastq_1.name.split('_')[0]  // get sample name
+                [ meta, fastq_1, fastq_2 ] }
+        .set { input }
+
+    MERGEFASTQ ( input )
+}
+
+//workflow {
+//    test_mergefastq()
+//}
+//nextflow run main.nf -process.echo -profile docker 
diff --git a/tests/modules/nf-core/mergefastq/nextflow.config b/tests/modules/nf-core/mergefastq/nextflow.config
new file mode 100644
index 000000000000..8324dbfee482
--- /dev/null
+++ b/tests/modules/nf-core/mergefastq/nextflow.config
@@ -0,0 +1,60 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
+
+
+params {
+    enable_conda = false
+    outdir = "output"
+}
+
+profiles {
+    debug { process.beforeScript = 'echo $HOSTNAME' }
+    conda {
+        params.enable_conda    = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    docker {
+        docker.enabled         = true
+        docker.userEmulation   = true
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    singularity {
+        singularity.enabled    = true
+        singularity.autoMounts = true
+        docker.enabled         = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    podman {
+        podman.enabled         = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
+    shifter {
+        shifter.enabled        = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        charliecloud.enabled   = false
+    }
+    charliecloud {
+        charliecloud.enabled   = true
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+    }
+}
diff --git a/tests/modules/nf-core/mergefastq/test.yml b/tests/modules/nf-core/mergefastq/test.yml
new file mode 100644
index 000000000000..11f619fa5fa4
--- /dev/null
+++ b/tests/modules/nf-core/mergefastq/test.yml
@@ -0,0 +1,7 @@
+- name: mergefastq
+  command: nextflow run ./tests/modules/nf-core/mergefastq -entry test_mergefastq -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mergefastq/nextflow.config
+  tags:
+    - mergefastq
+  files:
+    - path: output/mergefastq/Sample1-T2_L000_R1_mrg.fastq.gz
+    - path: output/mergefastq/versions.yml
diff --git a/tests/modules/nf-core/tabix/bgziptabix/main.nf b/tests/modules/nf-core/tabix/bgziptabix/main.nf
index f4bc4754bf58..26e17101f8b9 100644
--- a/tests/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/tests/modules/nf-core/tabix/bgziptabix/main.nf
@@ -2,15 +2,12 @@
 
 nextflow.enable.dsl = 2
 
-include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_TBI } from '../../../../../modules/nf-core/tabix/bgziptabix/main.nf'
-include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_CSI } from '../../../../../modules/nf-core/tabix/bgziptabix/main.nf'
+include { TABIX_BGZIPTABIX } from '../../../../../modules/nf-core/tabix/bgziptabix/main.nf'
 
 workflow test_tabix_bgziptabix {
     input = [ [ id:'test' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
             ]
 
-    TABIX_BGZIPTABIX_TBI ( input )
-    TABIX_BGZIPTABIX_CSI ( input )
-
+    TABIX_BGZIPTABIX ( input )
 }
diff --git a/tests/modules/nf-core/tabix/bgziptabix/nextflow.config b/tests/modules/nf-core/tabix/bgziptabix/nextflow.config
index 7830e9153461..041bfa6acc1c 100644
--- a/tests/modules/nf-core/tabix/bgziptabix/nextflow.config
+++ b/tests/modules/nf-core/tabix/bgziptabix/nextflow.config
@@ -2,12 +2,8 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: TABIX_BGZIPTABIX_TBI {
+    withName: TABIX_BGZIPTABIX {
         ext.args2 = '-p vcf'
     }
 
-    withName: TABIX_BGZIPTABIX_CSI {
-        ext.args2 = '-p vcf --csi'
-    }
-
 }
diff --git a/tests/modules/nf-core/tabix/bgziptabix/test.yml b/tests/modules/nf-core/tabix/bgziptabix/test.yml
index 6bbfb09c798d..78ce288b3218 100644
--- a/tests/modules/nf-core/tabix/bgziptabix/test.yml
+++ b/tests/modules/nf-core/tabix/bgziptabix/test.yml
@@ -5,8 +5,6 @@
     - tabix
   files:
     - path: output/tabix/test.vcf.gz
-      md5sum: 02aff9ae43faf2594f28e2cf87b32ba9
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
     - path: output/tabix/test.vcf.gz.tbi
-      md5sum: d22e5b84e4fcd18792179f72e6da702e
-    - path: output/tabix/test.vcf.gz.csi
-      md5sum: 6f733d80ee760fcc8fdbe504a03f2640
+      md5sum: 36e11bf96ed0af4a92caa91a68612d64
diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
deleted file mode 100644
index d6af5c2c9998..000000000000
--- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ /dev/null
@@ -1,170 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { VCF_ANNOTATE_ENSEMBLVEP_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf'
-
-workflow vcf_annotate_ensemblvep_snpeff_vep {
-    input = Channel.of([
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ],[
-        [ id:'custom_test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-        [
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true)
-        ]
-    ])
-
-    VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
-        input,
-        [[],[]],
-        "WBcel235",
-        "caenorhabditis_elegans",
-        "108",
-        [],
-        [],
-        [],
-        [],
-        ["ensemblvep"],
-        5
-    )
-}
-
-workflow vcf_annotate_ensemblvep_snpeff_snpeff {
-    input = Channel.of([
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ],[
-        [ id:'custom_test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-        [
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true)
-        ]
-    ])
-
-    VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
-        input,
-        [[],[]],
-        [],
-        [],
-        [],
-        [],
-        [],
-        "WBcel235.99",
-        [],
-        ["snpeff"],
-        5
-    )
-}
-
-workflow vcf_annotate_ensemblvep_snpeff_both {
-    input = Channel.of([
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ],[
-        [ id:'custom_test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-        [
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true)
-        ]
-    ])
-
-    VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
-        input,
-        [[],[]],
-        "WBcel235",
-        "caenorhabditis_elegans",
-        "108",
-        [],
-        [],
-        "WBcel235.99",
-        [],
-        ["snpeff", "ensemblvep"],
-        5
-    )
-}
-
-workflow vcf_annotate_ensemblvep_snpeff_large_chunks {
-    input = Channel.of([
-        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ],[
-        [ id:'custom_test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-        [
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true)
-        ]
-    ])
-
-    fasta = [
-        [id:"fasta"],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
-        input,
-        fasta,
-        "WBcel235",
-        "caenorhabditis_elegans",
-        "108",
-        [],
-        [],
-        [],
-        [],
-        ["ensemblvep"],
-        100
-    )
-}
-
-workflow vcf_annotate_ensemblvep_snpeff_no_scatter {
-    input = Channel.of([
-        [ id:'test1' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
-        []
-    ],[
-        [ id:'custom_test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true),
-        [
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true),
-            file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true)
-        ]
-    ])
-
-    fasta = [
-        [id:"fasta"],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    VCF_ANNOTATE_ENSEMBLVEP_SNPEFF (
-        input,
-        fasta,
-        "WBcel235",
-        "caenorhabditis_elegans",
-        "108",
-        [],
-        [],
-        [],
-        [],
-        ["ensemblvep"],
-        []
-    )
-}
diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config
deleted file mode 100644
index e48fa306d676..000000000000
--- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config
+++ /dev/null
@@ -1,21 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: ENSEMBLVEP_VEP {
-        container = 'docker.io/nfcore/vep:108.2.WBcel235'
-        ext.args = {[
-            "--vcf --offline",
-            meta.id.startsWith("custom_test") ? "--custom test3.vcf.gz,,vcf,exact,0,TOPMED" : ""
-        ].join(" ")}
-    }
-
-    withName: SNPEFF_SNPEFF {
-        container = 'docker.io/nfcore/snpeff:5.0.WBcel235'
-    }
-
-    withName: BCFTOOLS_CONCAT {
-        ext.prefix = { "${meta.id}_concat" }
-    }
-
-}
diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml
deleted file mode 100644
index 92fa202cb90d..000000000000
--- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml
+++ /dev/null
@@ -1,384 +0,0 @@
-- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_vep
-  command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_vep -c ./tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-    - bcftools/pluginscatter
-    - bcftools/sort
-    - ensemblvep
-    - ensemblvep/vep
-    - snpeff
-    - snpeff/snpeff
-    - subworkflows
-    - subworkflows/vcf_annotate_ensemblvep_snpeff
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/bcftools/custom_test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/custom_test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/custom_test1_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test1_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test1_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test1_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/tabix/custom_test.vcf.gz.tbi
-    - path: output/tabix/test.vcf.gz.tbi
-- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_snpeff
-  command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_snpeff -c ./tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-    - bcftools/pluginscatter
-    - bcftools/sort
-    - ensemblvep
-    - ensemblvep/vep
-    - snpeff
-    - snpeff/snpeff
-    - subworkflows
-    - subworkflows/vcf_annotate_ensemblvep_snpeff
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/bcftools/custom_test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test0_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test0_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/custom_test0_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/custom_test1_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test1_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/custom_test1_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/snpEff_summary.html
-      contains:
-        - '<style type="text/css">'
-    - path: output/snpeff/test0_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/test0_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/test0_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/test1_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/test1_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/test1_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/tabix/custom_test.vcf.gz.tbi
-
-- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_both
-  command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_both -c ./tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-    - bcftools/pluginscatter
-    - bcftools/sort
-    - ensemblvep
-    - ensemblvep/vep
-    - snpeff
-    - snpeff/snpeff
-    - subworkflows
-    - subworkflows/vcf_annotate_ensemblvep_snpeff
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/bcftools/custom_test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test1.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/custom_test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/custom_test1_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test1_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test1_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test1_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test0_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test0_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/custom_test0_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/custom_test1_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/custom_test1_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/custom_test1_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/snpEff_summary.html
-      contains:
-        - '<style type="text/css">'
-    - path: output/snpeff/test0_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/test0_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/test0_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/snpeff/test1_annotated.ann.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/snpeff/test1_annotated.csv
-      contains:
-        - "# Summary table"
-    - path: output/snpeff/test1_annotated.genes.txt
-      md5sum: 130536bf0237d7f3f746d32aaa32840a
-    - path: output/tabix/custom_test.vcf.gz.tbi
-    - path: output/tabix/test.vcf.gz.tbi
-- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_large_chunks
-  command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_large_chunks -c ./tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-    - bcftools/pluginscatter
-    - bcftools/sort
-    - ensemblvep
-    - ensemblvep/vep
-    - snpeff
-    - snpeff/snpeff
-    - subworkflows
-    - subworkflows/vcf_annotate_ensemblvep_snpeff
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/bcftools/custom_test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/custom_test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test0.vcf
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/bcftools/test_concat.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/custom_test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test0_annotated.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test0_annotated.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/tabix/custom_test.vcf.gz.tbi
-    - path: output/tabix/test.vcf.gz.tbi
-- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_no_scatter
-  command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_no_scatter -c ./tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/concat
-    - bcftools/pluginscatter
-    - bcftools/sort
-    - ensemblvep
-    - ensemblvep/vep
-    - snpeff
-    - snpeff/snpeff
-    - subworkflows
-    - subworkflows/vcf_annotate_ensemblvep_snpeff
-    - tabix
-    - tabix/tabix
-  files:
-    - path: output/ensemblvep/custom_test.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/custom_test.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/ensemblvep/test1.summary.html
-      contains:
-        - "<html>"
-        - "<head>"
-    - path: output/ensemblvep/test1.vcf.gz
-      contains:
-        - "##fileformat=VCFv4.2"
-        - '##FILTER=<ID=PASS,Description="All filters passed">'
-    - path: output/tabix/custom_test.vcf.gz.tbi
-    - path: output/tabix/test1.vcf.gz.tbi