diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 69e685440..d75c30f7a 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/eager, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/eager issues](https://github.com/nf-core/eager/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/eager repository](https://github.com/nf-core/eager) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -40,7 +40,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 2a999dcee..985adf2dd 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/eage
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/eager _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index bac036714..454f353ea 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,18 +1,35 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/eager'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/eager' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b9827c75d..682d9e7f3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -7,9 +7,12 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -17,39 +20,75 @@ concurrency:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/eager') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
         PARAMS:
-          - "-profile test,docker --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
-          - "-profile test,docker --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
-          - "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
-          - "-profile test,docker --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
-          - "-profile test,docker --mapping_tool circularmapper --skip_preprocessing --convert_inputbam --fasta_circular_target 'NC_007596.2' --fasta_circularmapper_elongationfactor 500"
-          - "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
-          - "-profile test_humanbam,docker --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
-          - "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref
+          - " --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
+          - " --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
+          - " --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
+          - " --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
+          - " --mapping_tool circularmapper --skip_preprocessing --convert_inputbam --fasta_circular_target 'NC_007596.2' --fasta_circularmapper_elongationfactor 500"
+          - "_humanbam --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
+          - "_humanbam --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
+          - "_multiref" ## TODO add damage manipulation here instead once it goes multiref
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
+      - name: Set up 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
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} --outdir ./results ${{ matrix.PARAMS }}
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{matrix.profile}},${{ matrix.test_name }}${{ matrix.PARAMS }} --outdir ./results
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d6442..713dc3e73 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe880..a502573c5 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f5..42e519bfa 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 03ecfcf72..c6ba35df4 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 000000000..e8aafe44d
--- /dev/null
+++ b/.github/workflows/template_version_comment.yml
@@ -0,0 +1,46 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Read template version from .nf-core.yml
+        uses: nichmor/minimal-read-yaml@v0.0.2
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          contains(env.OUTPUT, 'nf-core')
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+          #
diff --git a/.gitignore b/.gitignore
index 5124c9ac7..23b0c7de9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,5 @@ results/
 testing/
 testing*
 *.pyc
+null/
+.nf-test*
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a1821a..461186376 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,14 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index c75905a2f..4ec9275ea 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,7 +1,19 @@
-repository_type: pipeline
-nf_core_version: "2.14.1"
-
+bump_version: null
 lint:
   nextflow_config:
     - config_defaults:
         - params.contamination_estimation_angsd_hapmap
+nf_core_version: 3.0.2
+org_path: null
+repository_type: pipeline
+template:
+  author: The nf-core/eager community
+  description: A fully reproducible and state-of-the-art ancient DNA analysis pipeline
+  force: false
+  is_nfcore: true
+  name: eager
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 3.0.0dev
+update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1dcd..9e9f0e1c4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CITATIONS.md b/CITATIONS.md
index 41c130a70..d89e5577a 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,7 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
diff --git a/README.md b/README.md
index 1c8931c3a..a4847775a 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/eager/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/eager/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/eager/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -116,8 +116,7 @@ nextflow run nf-core/eager \
 ```
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/eager/usage) and the [parameter documentation](https://nf-co.re/eager/parameters).
 
diff --git a/assets/schema_fasta.json b/assets/schema_fasta.json
index 54e00de8e..cbdd4639f 100644
--- a/assets/schema_fasta.json
+++ b/assets/schema_fasta.json
@@ -1,8 +1,8 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/eager/master/assets/schema_fasta.json",
-    "title": "nf-core/eager pipeline - params.fasta schema",
-    "description": "Schema for the file provided with params.fasta",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/eager/master/assets/schema_input.json",
+    "title": "nf-core/eager pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
         "type": "object",
@@ -11,7 +11,6 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "meta": ["id"],
-                "unique": true,
                 "errorMessage": "Reference name must be provided and cannot contain spaces."
             },
             "fasta": {
@@ -19,7 +18,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(na|asta|a|as)(\\.gz)?$",
                 "exists": true,
-                "unique": true,
                 "errorMessage": "Fasta files for the mapping reference must be provided with file extensions '.fasta', '.fa', '.fas', '.fna', '.fasta.gz','.fa.gz','.fas.gz', '.fna.gz' and cannot contain any spaces."
             },
             "fai": {
@@ -79,7 +77,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.bed(\\.gz)?$",
                 "exists": true,
-                "dependentRequired": ["pileupcaller_snpfile"],
                 "errorMessage": "SNP capture bed files for pileupcaller must not contain any spaces, have file extensions '.bed' or '.bed.gz' and be provided alongside a pileupcall_bedfile."
             },
             "pileupcaller_snpfile": {
@@ -87,7 +84,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.snp$",
                 "exists": true,
-                "dependentRequired": ["pileupcaller_bedfile"],
                 "errorMessage": "SNP panel files for pileupcaller must not contain any spaces, have file extension '.snp' and be provided alongside a pileupcaller_snpfile."
             },
             "hapmap_file": {
@@ -138,6 +134,13 @@
                 "errorMessage": "SNP annotation files for GATK must not contain any spaces and have file extension '.vcf'."
             }
         },
-        "required": ["reference_name", "fasta"]
-    }
+        "required": ["reference_name", "fasta"],
+        "dependentRequired": {
+            "pileupcaller_snpfile": ["pileupcaller_bedfile"],
+            "pileupcaller_bedfile": ["pileupcaller_snpfile"],
+            "bam": ["bam_reference_id"],
+            "bam_reference_id": ["bam"]
+        }
+    },
+    "uniqueEntries": ["reference_name", "fasta"]
 }
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 12da4fba1..673a694a2 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/eager/master/assets/schema_input.json",
     "title": "nf-core/eager pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -21,7 +21,6 @@
             },
             "lane": {
                 "type": "integer",
-                "unique": ["library_id"],
                 "meta": ["lane"],
                 "errorMessage": "Sequencing lane number must be provided and specified as an integer. If no lane information, specify 0."
             },
@@ -54,7 +53,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "exists": true,
-                "unique": true,
                 "errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
             },
             "r2": {
@@ -62,8 +60,6 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "exists": true,
-                "unique": true,
-                "dependentRequired": ["r1"],
                 "errorMessage": "FastQ file for reads 2 require files for reads 1, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
             },
             "bam": {
@@ -71,14 +67,11 @@
                 "format": "file-path",
                 "pattern": "^\\S+\\.bam$",
                 "exists": true,
-                "unique": true,
-                "dependentRequired": ["bam_reference_id"],
                 "errorMessage": "BAM files cannot contain any spaces and must have extension '.bam'."
             },
             "bam_reference_id": {
                 "type": "string",
                 "meta": ["bam_reference_id"],
-                "dependentRequired": ["bam"],
                 "errorMessage": "A BAM reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a BAM file."
             }
         },
@@ -98,6 +91,17 @@
             {
                 "required": ["bam"]
             }
-        ]
-    }
+        ],
+        "dependentRequired": {
+            "r2": ["r1"],
+            "bam": ["bam_reference_id"],
+            "bam_reference_id": ["bam"]
+        }
+    },
+    "allOf": [
+        { "uniqueEntries": ["lane", "library_id"] },
+        { "uniqueEntries": "r1" },
+        { "uniqueEntries": "r2" },
+        { "uniqueEntries": "bam" }
+    ]
 }
diff --git a/conf/base.config b/conf/base.config
index 27ddc6fd9..381127cf2 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -11,9 +11,9 @@
 process {
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -27,30 +27,31 @@ process {
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 4.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 4.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 4     * task.attempt }
+        memory = { 8.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 8    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 8    * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 16.h  * task.attempt }
+
     }
     withLabel:process_long {
-        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
+        time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        memory = { 200.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
new file mode 100644
index 000000000..b4034d824
--- /dev/null
+++ b/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/conf/modules.config b/conf/modules.config
index 09fbff1fc..3e3a55848 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -59,7 +59,6 @@ process {
             mode: params.publish_dir_mode,
         ]
     }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index f23998ca1..e358134ad 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,15 +10,18 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
diff --git a/conf/test_humanbam.config b/conf/test_humanbam.config
index b60988019..21c35179f 100644
--- a/conf/test_humanbam.config
+++ b/conf/test_humanbam.config
@@ -10,43 +10,46 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'Human BAM test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name                 = 'Human BAM test profile'
+    config_profile_description          = 'Minimal test dataset to check pipeline function'
 
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
+    input                               = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
+    fasta                               = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
 
     // Contamination estimation
     contamination_estimation_angsd_mapq = 0
     contamination_estimation_angsd_minq = 0
 
     // Qualimap
-    snpcapture_bed = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    snpcapture_bed                      = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
 
     // TODO Reactivate sexDet and genotyping params when those steps get implemented.
     // //Sex Determination
-    sexdeterrmine_bedfile = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    sexdeterrmine_bedfile               = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
     // // Genotyping
-    genotyping_pileupcaller_bedfile = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
-    genotyping_pileupcaller_snpfile = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
+    genotyping_pileupcaller_bedfile     = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz'
+    genotyping_pileupcaller_snpfile     = params.pipelines_testdata_base_path + 'eager/reference/Human/1240K_covered_in_JK2067_downsampled_s0.1.numeric_chromosomes.snp'
 
 
     // BAM filtering
-    run_bamfiltering                      = true
-    bamfiltering_minreadlength            = 30
-    bamfiltering_mappingquality           = 37
+    run_bamfiltering                    = true
+    bamfiltering_minreadlength          = 30
+    bamfiltering_mappingquality         = 37
 
     // Metagenomic screening
-    run_metagenomics                      = false
+    run_metagenomics                    = false
 }
diff --git a/conf/test_kraken2.config b/conf/test_kraken2.config
index 295913d10..b976d1797 100644
--- a/conf/test_kraken2.config
+++ b/conf/test_kraken2.config
@@ -11,20 +11,22 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 params {
-    config_profile_name        = 'Kraken2 test profile'
-    config_profile_description = 'Minimal test dataset to check the metagenomics kraken2 pipeline function'
-
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+    config_profile_name             = 'Kraken2 test profile'
+    config_profile_description      = 'Minimal test dataset to check the metagenomics kraken2 pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+    fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Metagenomics
     run_metagenomics                = true
diff --git a/conf/test_krakenuniq.config b/conf/test_krakenuniq.config
index 81ccc0c88..5b25c1d66 100644
--- a/conf/test_krakenuniq.config
+++ b/conf/test_krakenuniq.config
@@ -11,20 +11,23 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'KrakenUniq test profile'
-    config_profile_description = 'Minimal test dataset to check the metagenomics krakenuniq pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name             = 'KrakenUniq test profile'
+    config_profile_description      = 'Minimal test dataset to check the metagenomics krakenuniq pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+    fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Metagenomics
     run_metagenomics                = true
diff --git a/conf/test_malt.config b/conf/test_malt.config
index b1088f992..43b905cc9 100644
--- a/conf/test_malt.config
+++ b/conf/test_malt.config
@@ -11,20 +11,23 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'MALT test profile'
-    config_profile_description = 'Minimal test dataset to check the metagenomics MALT pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name             = 'MALT test profile'
+    config_profile_description      = 'Minimal test dataset to check the metagenomics MALT pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+    fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Metagenomics
     run_metagenomics                = true
diff --git a/conf/test_metaphlan.config b/conf/test_metaphlan.config
index 89c34a2d3..85343cb79 100644
--- a/conf/test_metaphlan.config
+++ b/conf/test_metaphlan.config
@@ -11,20 +11,23 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'MetaPhlAn4 test profile'
-    config_profile_description = 'Minimal test dataset to check the metagenomics metaphlan4 pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name             = 'MetaPhlAn4 test profile'
+    config_profile_description      = 'Minimal test dataset to check the metagenomics metaphlan4 pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
+    input                           = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_v3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
+    fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Metagenomics
     run_metagenomics                = true
diff --git a/conf/test_multiref.config b/conf/test_multiref.config
index 0ef6417b6..6917a1a65 100644
--- a/conf/test_multiref.config
+++ b/conf/test_multiref.config
@@ -11,28 +11,29 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name         = 'Test profile'
+    config_profile_description  = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_multilane_multilib.tsv'
+    input                       = params.pipelines_testdata_base_path + 'eager/testdata/Mammoth/samplesheet_multilane_multilib.tsv'
 
     // Genome references
-    fasta_sheet = params.pipelines_testdata_base_path + 'eager/reference/reference_sheet_multiref.csv'
+    fasta_sheet                 = params.pipelines_testdata_base_path + 'eager/reference/reference_sheet_multiref.csv'
 
     // BAM filtering
-    run_bamfiltering                      = true
-    bamfiltering_minreadlength            = 30
-    bamfiltering_mappingquality           = 37
+    run_bamfiltering            = true
+    bamfiltering_minreadlength  = 30
+    bamfiltering_mappingquality = 37
 
     // Metagenomics
-    run_metagenomics                      = false
-
-
+    run_metagenomics            = false
 }
diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index 7f8f7ae2a..976074844 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -10,28 +10,31 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
+params {
+    config_profile_name                = 'Test profile'
+    config_profile_description         = 'Minimal test dataset to check pipeline function'
 
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
+    input                              = params.pipelines_testdata_base_path + 'eager/testdata/Human/human_design_bam_eager3.tsv'
 
     // Genome references
-    fasta = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
+    fasta                              = params.pipelines_testdata_base_path + 'eager/reference/Human/hs37d5_chr21-MT.fa.gz'
 
-    skip_preprocessing      = true
-    skip_deduplication      = true
-    skip_qualimap           = true
-    skip_damage_calculation = true
-    mapstats_skip_preseq    = true
+    skip_preprocessing                 = true
+    skip_deduplication                 = true
+    skip_qualimap                      = true
+    skip_damage_calculation            = true
+    mapstats_skip_preseq               = true
 
     run_fastq_sharding                 = false
     run_bamfiltering                   = false
@@ -42,5 +45,4 @@ params {
     run_mapdamage_rescaling            = false
     run_pmd_filtering                  = false
     run_trim_bam                       = false
-
 }
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
index 361d0e47a..000000000
Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ
diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png
deleted file mode 100755
index cb39ebb80..000000000
Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ
diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png
deleted file mode 100755
index a4b89bf56..000000000
Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ
diff --git a/docs/output.md b/docs/output.md
index 32b9f150b..70aeb3790 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -31,18 +31,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
-FastQC results in the `raw/` directory contain the results of running FastQC on the 'raw' input files (with no processing by the pipeline). The `processed/` directory is for reads run through either fastp or AdapterRemoval preprocessing, and therefore will only be present if preprocessing is executed. These FastQC results occur in both html (the report) and .zip format (raw data).
-
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
-
 ### MultiQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index 3859cedff..133136506 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -149,9 +149,9 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run nf-core/eager -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
@@ -263,14 +263,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config
 
 If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
 
-## Azure Resource Requests
-
-To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.
-We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required.
-
-Note that the choice of VM size depends on your quota and the overall workload during the analysis.
-For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes).
-
 ## Running in the background
 
 Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
diff --git a/main.nf b/main.nf
index 4c541f62c..964022e54 100644
--- a/main.nf
+++ b/main.nf
@@ -9,8 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -20,7 +18,6 @@ nextflow.enable.dsl = 2
 include { EAGER  } from './workflows/eager'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_eager_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_eager_pipeline'
-
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_eager_pipeline'
 
 /*
@@ -58,10 +55,8 @@ workflow NFCORE_EAGER {
         samplesheet_fastqs,
         samplesheet_bams
     )
-
     emit:
     multiqc_report = EAGER.out.multiqc_report // channel: /path/to/multiqc_report.html
-
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -72,13 +67,11 @@ workflow NFCORE_EAGER {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
@@ -93,7 +86,6 @@ workflow {
         PIPELINE_INITIALISATION.out.samplesheet_fastqs,
         PIPELINE_INITIALISATION.out.samplesheet_bams,
     )
-
     //
     // SUBWORKFLOW: Run completion tasks
     //
diff --git a/modules.json b/modules.json
index a2fc85bbb..3a7ce7a3c 100644
--- a/modules.json
+++ b/modules.json
@@ -147,7 +147,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "freebayes": {
@@ -222,7 +222,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "picard/createsequencedictionary": {
@@ -366,17 +366,17 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38a9..691d4c763 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d79f1c862..d8989f481 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e06..4827da7af 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index 70edae4d9..e9d79a074 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -23,17 +23,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
+                { assert process.success },
+                // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+                // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+                // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
-            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
-            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
-            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
-            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
-            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
-            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
-            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
-            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
+                { assert process.success },
+                { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+                { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+                { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+                { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+                { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+                { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+                { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+                { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+                { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-
-            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
-            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
-            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-
-            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
+                { assert process.success },
+                { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+                { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+                { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         then {
             assertAll (
-            { assert process.success },
-            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
-                                process.out.zip.collect { file(it[1]).getName() } +
-                                process.out.versions ).match("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 86f7c3115..d5db3092f 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ca39fb67e..6f5b867b7 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 47ac352f9..cc0643e1d 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
@@ -44,7 +52,7 @@ process MULTIQC {
     stub:
     """
     mkdir multiqc_data
-    touch multiqc_plots
+    mkdir multiqc_plots
     touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 45a9bc35e..b16c18792 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index f1c4242ef..33316a7dd 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index bfebd8029..2fcbb5ff7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 000000000..c537a6a3e
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index c8a86d059..89b77adc6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,29 +57,22 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null
     config_profile_description = null
+
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
 
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
+    validate_params            = true
 
     // References
     save_reference = false
@@ -274,20 +267,6 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load nf-core/eager custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/eager.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/eager profiles: ${params.custom_config_base}/pipeline/eager.config")
-}
-
 // Additional configs for subworkflows
 includeConfig 'subworkflows/nf-core/bam_split_by_region/nextflow.config'
 includeConfig 'subworkflows/nf-core/bam_docounts_contamination_angsd/nextflow.config'
@@ -307,7 +286,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -404,25 +383,24 @@ profiles {
     test_metaphlan  { includeConfig 'conf/test_metaphlan.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
+// Load nf-core/eager custom profiles from different institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/eager.config" : "/dev/null"
+
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
+includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -434,8 +412,15 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = """\
+bash
+
+set -e # Exit if a tool returns a non-zero status/exit code
+set -u # Treat unset variables and parameters as an error
+set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+set -C # No clobber - prevent output redirection from overwriting files.
+"""
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -464,43 +449,46 @@ manifest {
     homePage        = 'https://github.com/nf-core/eager'
     description     = """A fully reproducible and state-of-the-art ancient DNA analysis pipeline"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
     version         = '3.0.0dev'
     doi             = '10.7717/peerj.10947'
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
+validation {
+    defaultIgnoreParams = ["genomes"]
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 818210161..394c63a5b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/eager/master/nextflow_schema.json",
     "title": "nf-core/eager pipeline parameters",
     "description": "A fully reproducible and state-of-the-art ancient DNA analysis pipeline",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -205,41 +205,6 @@
                 }
             }
         },
-        "max_job_request_options": {
-            "title": "Max job request options",
-            "type": "object",
-            "fa_icon": "fab fa-acquisitions-incorporated",
-            "description": "Set the top limit for requested resources for any single job.",
-            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
-            "properties": {
-                "max_cpus": {
-                    "type": "integer",
-                    "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
-                    "fa_icon": "fas fa-microchip",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
-                },
-                "max_memory": {
-                    "type": "string",
-                    "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
-                    "fa_icon": "fas fa-memory",
-                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
-                },
-                "max_time": {
-                    "type": "string",
-                    "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
-                    "fa_icon": "far fa-clock",
-                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
-                    "hidden": true,
-                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
-                }
-            }
-        },
         "generic_options": {
             "title": "Generic options",
             "type": "object",
@@ -247,12 +212,6 @@
             "description": "Less common options for the pipeline, typically set in a config file.",
             "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
             "properties": {
-                "help": {
-                    "type": "boolean",
-                    "description": "Display help text.",
-                    "fa_icon": "fas fa-question-circle",
-                    "hidden": true
-                },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
@@ -328,27 +287,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -1568,61 +1506,58 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         },
         {
-            "$ref": "#/definitions/preprocessing"
+            "$ref": "#/$defs/preprocessing"
         },
         {
-            "$ref": "#/definitions/mapping"
+            "$ref": "#/$defs/mapping"
         },
         {
-            "$ref": "#/definitions/bam_filtering"
+            "$ref": "#/$defs/bam_filtering"
         },
         {
-            "$ref": "#/definitions/metagenomics"
+            "$ref": "#/$defs/metagenomics"
         },
         {
-            "$ref": "#/definitions/deduplication"
+            "$ref": "#/$defs/deduplication"
         },
         {
-            "$ref": "#/definitions/damage_manipulation"
+            "$ref": "#/$defs/damage_manipulation"
         },
         {
-            "$ref": "#/definitions/genotyping"
+            "$ref": "#/$defs/genotyping"
         },
         {
-            "$ref": "#/definitions/mitochondrial_to_nuclear_ratio"
+            "$ref": "#/$defs/mitochondrial_to_nuclear_ratio"
         },
         {
-            "$ref": "#/definitions/mapping_statistics"
+            "$ref": "#/$defs/mapping_statistics"
         },
         {
-            "$ref": "#/definitions/adna_damage_analysis"
+            "$ref": "#/$defs/adna_damage_analysis"
         },
         {
-            "$ref": "#/definitions/feature_annotation_statistics"
+            "$ref": "#/$defs/feature_annotation_statistics"
         },
         {
-            "$ref": "#/definitions/host_removal"
+            "$ref": "#/$defs/host_removal"
         },
         {
-            "$ref": "#/definitions/contamination_estimation"
+            "$ref": "#/$defs/contamination_estimation"
         },
         {
-            "$ref": "#/definitions/human_sex_determination"
+            "$ref": "#/$defs/human_sex_determination"
         }
     ]
 }
diff --git a/subworkflows/local/reference_indexing_multi.nf b/subworkflows/local/reference_indexing_multi.nf
index 00276a5b9..c629c1df0 100644
--- a/subworkflows/local/reference_indexing_multi.nf
+++ b/subworkflows/local/reference_indexing_multi.nf
@@ -7,9 +7,9 @@ include { BWA_INDEX                       } from '../../modules/nf-core/bwa/inde
 include { BOWTIE2_BUILD                   } from '../../modules/nf-core/bowtie2/build/main'
 include { SAMTOOLS_FAIDX                  } from '../../modules/nf-core/samtools/faidx/main'
 include { PICARD_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/picard/createsequencedictionary/main'
+include { samplesheetToList               } from 'plugin/nf-schema'
 
 workflow REFERENCE_INDEXING_MULTI {
-
     take:
     referencesheet // file: /path/to/name.{csv,tsv}
 
@@ -17,28 +17,28 @@ workflow REFERENCE_INDEXING_MULTI {
     ch_versions = Channel.empty()
 
     // Import reference sheet and change empty arrays to empty strings for compatibility with single reference input
-    ch_splitreferencesheet_for_branch = Channel.fromSamplesheet("fasta_sheet")
-                                    .map{
-                                        meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
-                                            meta.ploidy                    = meta.genotyping_ploidy != null ? meta.genotyping_ploidy : params.genotyping_reference_ploidy
-                                            fai                            = fai != [] ? fai : ""
-                                            dict                           = dict != [] ? dict : ""
-                                            mapper_index                   = mapper_index != [] ? mapper_index : ""
-                                            circular_target                = circular_target != [] ? circular_target : ""
-                                            circularmapper_elongatedfasta = circularmapper_elongatedfasta != [] ? circularmapper_elongatedfasta : ""
-                                            circularmapper_elongatedindex = circularmapper_elongatedindex != [] ? circularmapper_elongatedindex : ""
-                                            mitochondrion                  = mitochondrion != [] ? mitochondrion : ""
-                                            capture_bed                    = capture_bed != [] ? capture_bed : ""
-                                            pileupcaller_bed               = pileupcaller_bed != [] ? pileupcaller_bed : ""
-                                            pileupcaller_snp               = pileupcaller_snp != [] ? pileupcaller_snp : ""
-                                            hapmap                         = hapmap != [] ? hapmap : ""
-                                            pmd_masked_fasta               = pmd_masked_fasta != [] ? pmd_masked_fasta : ""
-                                            pmd_bed_for_masking            = pmd_bed_for_masking != [] ? pmd_bed_for_masking : ""
-                                            sexdet_bed                     = sexdet_bed != [] ? sexdet_bed : ""
-                                            bedtools_feature               = bedtools_feature != [] ? bedtools_feature : ""
-                                            genotyping_gatk_dbsnp          = genotyping_gatk_dbsnp != [] ? genotyping_gatk_dbsnp : ""
-                                        [ meta - meta.subMap('genotyping_ploidy'), fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ]
-                                    }
+    ch_splitreferencesheet_for_branch = Channel
+        .fromList(samplesheetToList(referencesheet, "${projectDir}/assets/schema_fasta.json"))
+        .map { meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
+            meta.ploidy = meta.genotyping_ploidy != null ? meta.genotyping_ploidy : params.genotyping_reference_ploidy
+            fai = fai != [] ? fai : ""
+            dict = dict != [] ? dict : ""
+            mapper_index = mapper_index != [] ? mapper_index : ""
+            circular_target = circular_target != [] ? circular_target : ""
+            circularmapper_elongatedfasta = circularmapper_elongatedfasta != [] ? circularmapper_elongatedfasta : ""
+            circularmapper_elongatedindex = circularmapper_elongatedindex != [] ? circularmapper_elongatedindex : ""
+            mitochondrion = mitochondrion != [] ? mitochondrion : ""
+            capture_bed = capture_bed != [] ? capture_bed : ""
+            pileupcaller_bed = pileupcaller_bed != [] ? pileupcaller_bed : ""
+            pileupcaller_snp = pileupcaller_snp != [] ? pileupcaller_snp : ""
+            hapmap = hapmap != [] ? hapmap : ""
+            pmd_masked_fasta = pmd_masked_fasta != [] ? pmd_masked_fasta : ""
+            pmd_bed_for_masking = pmd_bed_for_masking != [] ? pmd_bed_for_masking : ""
+            sexdet_bed = sexdet_bed != [] ? sexdet_bed : ""
+            bedtools_feature = bedtools_feature != [] ? bedtools_feature : ""
+            genotyping_gatk_dbsnp = genotyping_gatk_dbsnp != [] ? genotyping_gatk_dbsnp : ""
+            [meta - meta.subMap('genotyping_ploidy'), fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp]
+        }
 
     // GENERAL DESCRIPTION FOR NEXT SECTIONS
     // This will be the same scheme for all other generation steps, i.e.
@@ -51,44 +51,38 @@ workflow REFERENCE_INDEXING_MULTI {
     // DECOMPRESSION
     //
 
-    ch_input_from_referencesheet = ch_splitreferencesheet_for_branch
-                            .multiMap {
-                                meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
-                                generated:            [ meta, fasta, fai, dict, mapper_index ]
-                                circularmapper:       [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
-                                mitochondrion_header: [ meta, mitochondrion ]
-                                angsd_hapmap:         [ meta, hapmap ]
-                                pmd_masked_fasta:     [ meta, pmd_masked_fasta ]
-                                pmd_bed_for_masking:  [ meta, pmd_bed_for_masking ]
-                                snp_bed:              [ meta, capture_bed ]
-                                pileupcaller_bed_snp: [ meta, pileupcaller_bed, pileupcaller_snp ]
-                                sexdeterrmine_bed:    [ meta, sexdet_bed ]
-                                bedtools_feature:     [ meta, bedtools_feature ]
-                                dbsnp:                [ meta, genotyping_gatk_dbsnp ]
-                            }
+    ch_input_from_referencesheet = ch_splitreferencesheet_for_branch.multiMap { meta, fasta, fai, dict, mapper_index, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex, mitochondrion, capture_bed, pileupcaller_bed, pileupcaller_snp, hapmap, pmd_masked_fasta, pmd_bed_for_masking, sexdet_bed, bedtools_feature, genotyping_gatk_dbsnp ->
+        generated: [meta, fasta, fai, dict, mapper_index]
+        circularmapper: [meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex]
+        mitochondrion_header: [meta, mitochondrion]
+        angsd_hapmap: [meta, hapmap]
+        pmd_masked_fasta: [meta, pmd_masked_fasta]
+        pmd_bed_for_masking: [meta, pmd_bed_for_masking]
+        snp_bed: [meta, capture_bed]
+        pileupcaller_bed_snp: [meta, pileupcaller_bed, pileupcaller_snp]
+        sexdeterrmine_bed: [meta, sexdet_bed]
+        bedtools_feature: [meta, bedtools_feature]
+        dbsnp: [meta, genotyping_gatk_dbsnp]
+    }
 
     // Detect if fasta is gzipped or not
-    ch_fasta_for_gunzip = ch_input_from_referencesheet.generated
-                            .branch {
-                                meta, fasta, fai, dict, mapper_index ->
-                                    forgunzip: fasta.extension == "gz"
-                                    skip: true
-                            }
+    ch_fasta_for_gunzip = ch_input_from_referencesheet.generated.branch { meta, fasta, fai, dict, mapper_index ->
+        forgunzip: fasta.extension == "gz"
+        skip: true
+    }
 
     // Pull out name/file to match cardinality for GUNZIP module
-    ch_gunzip_input = ch_fasta_for_gunzip.forgunzip
-        .multiMap {
-            meta, fasta, fai, dict, mapper_index ->
-                gunzip:    [ meta, fasta ]
-                remainder: [ meta, fai, dict, mapper_index ]
-        }
+    ch_gunzip_input = ch_fasta_for_gunzip.forgunzip.multiMap { meta, fasta, fai, dict, mapper_index ->
+        gunzip: [meta, fasta]
+        remainder: [meta, fai, dict, mapper_index]
+    }
 
 
-    GUNZIP_FASTA ( ch_gunzip_input.gunzip )
-    ch_version = ch_versions.mix( GUNZIP_FASTA.out.versions )
+    GUNZIP_FASTA(ch_gunzip_input.gunzip)
+    ch_version = ch_versions.mix(GUNZIP_FASTA.out.versions)
 
     // Mix back gunzipped fasta with remaining files, and then mix back with pre-gunzipped references
-    ch_gunzippedfasta_formix = GUNZIP_FASTA.out.gunzip.join( ch_gunzip_input.remainder, failOnMismatch: true )
+    ch_gunzippedfasta_formix = GUNZIP_FASTA.out.gunzip.join(ch_gunzip_input.remainder, failOnMismatch: true)
     ch_fasta_for_faiindexing = ch_fasta_for_gunzip.skip.mix(ch_gunzippedfasta_formix)
 
     //
@@ -96,33 +90,27 @@ workflow REFERENCE_INDEXING_MULTI {
     //
 
     // Separate out non-faidxed references
-    ch_fasta_for_faidx = ch_fasta_for_faiindexing
-        .branch {
-            meta, fasta, fai, dict, mapper_index ->
-                forfaidx: fai == ""
-                skip: true
-        }
+    ch_fasta_for_faidx = ch_fasta_for_faiindexing.branch { meta, fasta, fai, dict, mapper_index ->
+        forfaidx: fai == ""
+        skip: true
+    }
 
     // Split channel to ensure cardinality matching
-    ch_faidx_input = ch_fasta_for_faidx
-        .forfaidx
-        .multiMap {
-            meta, fasta, fai, dict, mapper_index ->
-                faidx:      [ meta, fasta ]
-                remainder:  [ meta, fasta, dict, mapper_index ] // we drop fai here as we are going to make it
-        }
+    ch_faidx_input = ch_fasta_for_faidx.forfaidx.multiMap { meta, fasta, fai, dict, mapper_index ->
+        faidx: [meta, fasta]
+        remainder: [meta, fasta, dict, mapper_index]
+    }
 
-    SAMTOOLS_FAIDX ( ch_faidx_input.faidx, [ [], [] ] )
-    ch_version = ch_versions.mix( SAMTOOLS_FAIDX.out.versions )
+    SAMTOOLS_FAIDX(ch_faidx_input.faidx, [[], []])
+    ch_version = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
 
     // Rejoin output channel with main reference indicies channel elements
-    ch_faidxed_formix =  SAMTOOLS_FAIDX.out.fai
-                            .join( ch_faidx_input.remainder, failOnMismatch: true )
-                            .map {
-                                meta, fai, fasta, dict, mapper_index ->
+    ch_faidxed_formix = SAMTOOLS_FAIDX.out.fai
+        .join(ch_faidx_input.remainder, failOnMismatch: true)
+        .map { meta, fai, fasta, dict, mapper_index ->
 
-                                [ meta, fasta, fai, dict, mapper_index ]
-                            }
+            [meta, fasta, fai, dict, mapper_index]
+        }
 
     // Mix back newly faidx'd references with the pre-indexed ones
     ch_fasta_for_dictindexing = ch_fasta_for_faidx.skip.mix(ch_faidxed_formix)
@@ -131,31 +119,25 @@ workflow REFERENCE_INDEXING_MULTI {
     // INDEXING: dict
     //
 
-    ch_fasta_for_dict = ch_fasta_for_dictindexing
-        .branch {
-            meta, fasta, fai, dict, mapper_index ->
-                fordict: dict == ""
-                skip: true
-        }
+    ch_fasta_for_dict = ch_fasta_for_dictindexing.branch { meta, fasta, fai, dict, mapper_index ->
+        fordict: dict == ""
+        skip: true
+    }
 
-    ch_dict_input = ch_fasta_for_dict
-        .fordict
-        .multiMap {
-            meta, fasta, fai, dict, mapper_index ->
-                dict:      [ meta, fasta ]
-                remainder:  [ meta, fasta, fai, mapper_index ]
-        }
+    ch_dict_input = ch_fasta_for_dict.fordict.multiMap { meta, fasta, fai, dict, mapper_index ->
+        dict: [meta, fasta]
+        remainder: [meta, fasta, fai, mapper_index]
+    }
 
-    PICARD_CREATESEQUENCEDICTIONARY ( ch_dict_input.dict )
-    ch_version = ch_versions.mix( PICARD_CREATESEQUENCEDICTIONARY.out.versions )
+    PICARD_CREATESEQUENCEDICTIONARY(ch_dict_input.dict)
+    ch_version = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
 
-    ch_dicted_formix =  PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
-                            .join( ch_dict_input.remainder, failOnMismatch: true )
-                            .map {
-                                meta, dict, fasta, fai, mapper_index ->
+    ch_dicted_formix = PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict
+        .join(ch_dict_input.remainder, failOnMismatch: true)
+        .map { meta, dict, fasta, fai, mapper_index ->
 
-                                [ meta, fasta, fai, dict, mapper_index ]
-                            }
+            [meta, fasta, fai, dict, mapper_index]
+        }
 
     ch_dict_formapperindexing = ch_fasta_for_dict.skip.mix(ch_dicted_formix)
 
@@ -165,52 +147,47 @@ workflow REFERENCE_INDEXING_MULTI {
 
     // Generate mapper indicies if not supplied, and if supplied generate meta
 
-    ch_fasta_for_mapperindex = ch_dict_formapperindexing
-        .branch {
-            meta, fasta, fai, dict, mapper_index ->
-                forindex: mapper_index == ""
-                skip: true
-        }
+    ch_fasta_for_mapperindex = ch_dict_formapperindexing.branch { meta, fasta, fai, dict, mapper_index ->
+        forindex: mapper_index == ""
+        skip: true
+    }
 
-    ch_mapindex_input = ch_fasta_for_mapperindex
-        .forindex
-        .multiMap {
-            meta, fasta, fai, dict, mapper_index ->
-                index:      [ meta, fasta ]
-                remainder:  [ meta, fasta, fai, dict ]
-        }
+    ch_mapindex_input = ch_fasta_for_mapperindex.forindex.multiMap { meta, fasta, fai, dict, mapper_index ->
+        index: [meta, fasta]
+        remainder: [meta, fasta, fai, dict]
+    }
 
-    if ( params.mapping_tool == "bwaaln" || params.mapping_tool == "bwamem" || params.mapping_tool == "circularmapper" ) {
-        BWA_INDEX ( ch_mapindex_input.index )
-        ch_version = ch_versions.mix( BWA_INDEX.out.versions )
+    if (params.mapping_tool == "bwaaln" || params.mapping_tool == "bwamem" || params.mapping_tool == "circularmapper") {
+        BWA_INDEX(ch_mapindex_input.index)
+        ch_version = ch_versions.mix(BWA_INDEX.out.versions)
         ch_indexed_forremap = BWA_INDEX.out.index
-    } else if ( params.mapping_tool == "bowtie2" ) {
-        BOWTIE2_BUILD ( ch_mapindex_input.index )
-        ch_version = ch_versions.mix( BOWTIE2_BUILD.out.versions )
+    }
+    else if (params.mapping_tool == "bowtie2") {
+        BOWTIE2_BUILD(ch_mapindex_input.index)
+        ch_version = ch_versions.mix(BOWTIE2_BUILD.out.versions)
         ch_indexed_forremap = BOWTIE2_BUILD.out.index
     }
 
     ch_indexed_formix = ch_indexed_forremap
-                            .join( ch_mapindex_input.remainder, failOnMismatch: true )
-                            .map {
-                                meta, mapper_index, fasta, fai, dict ->
+        .join(ch_mapindex_input.remainder, failOnMismatch: true)
+        .map { meta, mapper_index, fasta, fai, dict ->
 
-                                [ meta, fasta, fai, dict, mapper_index ]
-                            }
+            [meta, fasta, fai, dict, mapper_index]
+        }
 
     ch_indexmapper_for_reference = ch_fasta_for_mapperindex.skip.mix(ch_indexed_formix)
 
     emit:
-    reference            = ch_indexmapper_for_reference                         // [ meta, fasta, fai, dict, mapindex ]
-    elongated_reference  = ch_input_from_referencesheet.circularmapper          // [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
-    mitochondrion_header = ch_input_from_referencesheet.mitochondrion_header    // [ meta, mitochondrion ]
-    hapmap               = ch_input_from_referencesheet.angsd_hapmap            // [ meta, hapmap ]
-    pmd_masked_fasta     = ch_input_from_referencesheet.pmd_masked_fasta        // [ meta, pmd_masked_fasta ]
-    pmd_bed_for_masking  = ch_input_from_referencesheet.pmd_bed_for_masking     // [ meta, pmd_bed_for_masking ]
-    snp_capture_bed      = ch_input_from_referencesheet.snp_bed                 // [ meta, capture_bed ]
-    pileupcaller_bed_snp = ch_input_from_referencesheet.pileupcaller_bed_snp    // [ meta, pileupcaller_bed, pileupcaller_snp ]
-    sexdeterrmine_bed    = ch_input_from_referencesheet.sexdeterrmine_bed       // [ meta, sexdet_bed ]
-    bedtools_feature     = ch_input_from_referencesheet.bedtools_feature        // [ meta, bedtools_feature ]
-    dbsnp                = ch_input_from_referencesheet.dbsnp                   // [ meta, genotyping_gatk_dbsnp ]
+    reference            = ch_indexmapper_for_reference // [ meta, fasta, fai, dict, mapindex ]
+    elongated_reference  = ch_input_from_referencesheet.circularmapper // [ meta, circular_target, circularmapper_elongatedfasta, circularmapper_elongatedindex ]
+    mitochondrion_header = ch_input_from_referencesheet.mitochondrion_header // [ meta, mitochondrion ]
+    hapmap               = ch_input_from_referencesheet.angsd_hapmap // [ meta, hapmap ]
+    pmd_masked_fasta     = ch_input_from_referencesheet.pmd_masked_fasta // [ meta, pmd_masked_fasta ]
+    pmd_bed_for_masking  = ch_input_from_referencesheet.pmd_bed_for_masking // [ meta, pmd_bed_for_masking ]
+    snp_capture_bed      = ch_input_from_referencesheet.snp_bed // [ meta, capture_bed ]
+    pileupcaller_bed_snp = ch_input_from_referencesheet.pileupcaller_bed_snp // [ meta, pileupcaller_bed, pileupcaller_snp ]
+    sexdeterrmine_bed    = ch_input_from_referencesheet.sexdeterrmine_bed // [ meta, sexdet_bed ]
+    bedtools_feature     = ch_input_from_referencesheet.bedtools_feature // [ meta, bedtools_feature ]
+    dbsnp                = ch_input_from_referencesheet.dbsnp // [ meta, genotyping_gatk_dbsnp ]
     versions             = ch_versions
 }
diff --git a/subworkflows/local/utils_nfcore_eager_pipeline/main.nf b/subworkflows/local/utils_nfcore_eager_pipeline/main.nf
index ac01b35c2..be91c2e6b 100644
--- a/subworkflows/local/utils_nfcore_eager_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_eager_pipeline/main.nf
@@ -8,29 +8,25 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-validation'
-include { fromSamplesheet           } from 'plugin/nf-validation'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
 include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
 include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
 include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
 include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs   // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
@@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    pre_help_text = nfCoreLogo(monochrome_logs)
-    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
-    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
 
     //
@@ -79,9 +69,9 @@ workflow PIPELINE_INITIALISATION {
     validateInputParameters()
 
     //
-    // Create channel from input file provided through params.input
+    // Create channel from input file provided through input
     //
-    ch_samplesheet = Channel.fromSamplesheet("input")
+    ch_samplesheet = Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
                                     .map {
                                         meta, r1, r2, bam ->
                                             meta.single_end = meta.pairment == "single" ? true : false
@@ -128,6 +118,10 @@ workflow PIPELINE_INITIALISATION {
                 }
             [ meta, r1, r2, bam ]
         }
+        .groupTuple()
+        .map { samplesheet ->
+            validateInputSamplesheet(samplesheet)
+        }
 
     // - Only single-ended specified for BAM files
     ch_samplesheet_for_branch.bam
@@ -160,9 +154,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -177,7 +171,6 @@ workflow PIPELINE_COMPLETION {
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     //
@@ -185,11 +178,18 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                multiqc_report.toList()
+            )
         }
 
         completionSummary(monochrome_logs)
-
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
@@ -201,9 +201,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -250,7 +250,7 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
+    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
@@ -282,7 +282,6 @@ def genomeExistsError() {
         error(error_string)
     }
 }
-
 //
 // Generate methods description for MultiQC
 //
@@ -324,8 +323,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f6..0fcbf7b3f 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,18 +2,13 @@
 // 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
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
     // Print workflow version and exit on --version
     //
     if (print_version) {
-        log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
         System.exit(0)
     }
 
@@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 // 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}"
@@ -76,13 +71,13 @@ def getWorkflowVersion() {
 // Dump pipeline parameters to a JSON file
 //
 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 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   = 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()
 }
 
@@ -90,37 +85,40 @@ 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)
         channels = config.channels
-    } catch(NullPointerException | IOException e) {
-        log.warn "Could not verify conda channel configuration."
-        return
+    }
+    catch (NullPointerException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // 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]))
-    }
+    def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order }
 
     if (channels_missing | channel_priority_violation) {
-        log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  There is a problem with your Conda configuration!\n\n" +
-            "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
-            "  Please refer to https://bioconda.github.io/\n" +
-            "  The observed channel order is \n" +
-            "  ${channels}\n" +
-            "  but the following channel order is required:\n" +
-            "  ${required_channels_in_order}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        log.warn """\
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+            There is a problem with your Conda configuration!
+            You will need to set-up the conda-forge and bioconda channels correctly.
+            Please refer to https://bioconda.github.io/
+            The observed channel order is
+            ${channels}
+            but the following channel order is required:
+            ${required_channels_in_order}
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        """.stripIndent(true)
     }
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf6..a09572e5b 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 14558c392..5cb7bafef 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,17 +2,13 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
 //  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 "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
-            "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
-            "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
-            "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
-            "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
-            "Please refer to the quick start section and usage docs for the pipeline.\n "
+        log.warn(
+            "[${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" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
         valid_config = false
     }
     return valid_config
@@ -52,12 +45,14 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
@@ -66,25 +61,21 @@ def checkProfileProvided(nextflow_cli_args) {
 //
 def workflowCitation() {
     def temp_doi_ref = ""
-    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Handling 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"
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+    }
+    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
 }
 
 //
 // 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 +93,8 @@ 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()
 }
 
@@ -113,8 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -122,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { processVersionsFromYAML(it) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -134,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
-        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>$group</b></p>\n"
-            summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
-                summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                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"
             }
-            summary_section += "    </dl>\n"
         }
-    }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
-    yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
-    yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
-    yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
-    yaml_file_text        += "plot_type: 'html'\n"
-    yaml_file_text        += "data: |\n"
-    yaml_file_text        += "${summary_section}"
+    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/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
 
     return yaml_file_text
 }
@@ -161,7 +154,7 @@ 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
         ${dashedLine(monochrome_logs)}
@@ -180,7 +173,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -188,7 +181,7 @@ 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"
@@ -200,54 +193,54 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -262,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -281,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
     misc_fields['Date Started']              = workflow.start
     misc_fields['Date Completed']            = workflow.complete
     misc_fields['Pipeline script file path'] = workflow.scriptFile
     misc_fields['Pipeline script hash ID']   = workflow.scriptId
-    if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
-    if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
-    if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
-    misc_fields['Nextflow Version']           = workflow.nextflow.version
-    misc_fields['Nextflow Build']             = workflow.nextflow.build
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
     misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
     def email_fields = [:]
@@ -338,39 +341,41 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // Render the sendmail template
     def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     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) {
+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 }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
-        } catch (all) {
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // 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()
 }
 
@@ -378,15 +383,17 @@ 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}-"
-        } else {
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
+        }
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
         }
-    } else {
-        log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
     }
 }
 
@@ -395,21 +402,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
-        summary << summary_params[group]
-    }
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
 
     def misc_fields = [:]
-    misc_fields['start']                                = workflow.start
-    misc_fields['complete']                             = workflow.complete
-    misc_fields['scriptfile']                           = workflow.scriptFile
-    misc_fields['scriptid']                             = workflow.scriptId
-    if (workflow.repository) misc_fields['repository']  = workflow.repository
-    if (workflow.commitId)   misc_fields['commitid']    = workflow.commitId
-    if (workflow.revision)   misc_fields['revision']    = workflow.revision
-    misc_fields['nxf_version']                          = workflow.nextflow.version
-    misc_fields['nxf_build']                            = workflow.nextflow.build
-    misc_fields['nxf_timestamp']                        = workflow.nextflow.timestamp
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
 
     def msg_fields = [:]
     msg_fields['version']      = getWorkflowVersion()
@@ -434,13 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 000000000..4994303ea
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 000000000..f7d9f0288
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 000000000..842dc432a
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 000000000..0907ac58f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c93..331e0d2f4 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65d1..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04f..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5784a33f2..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,200 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflows"
-    tag "subworkflows_nfcore"
-    tag "plugin/nf-validation"
-    tag "'plugin/nf-validation'"
-    tag "utils_nfvalidation_plugin"
-    tag "subworkflows/utils_nfvalidation_plugin"
-
-    test("Should run nothing") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-
-    test("Should run help") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with command") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } }
-            )
-        }
-    }
-
-    test("Should run help with extra text") {
-
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-            }
-            workflow {
-                """
-                help             = true
-                workflow_command = "nextflow run noorg/doesntexist"
-                pre_help_text    = "pre-help-text"
-                post_help_text   = "post-help-text"
-                validate_params  = false
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.exitStatus == 0 },
-                { assert workflow.stdout.any { it.contains('pre-help-text') } },
-                { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } },
-                { assert workflow.stdout.any { it.contains('Input/output options') } },
-                { assert workflow.stdout.any { it.contains('--outdir') } },
-                { assert workflow.stdout.any { it.contains('post-help-text') } }
-            )
-        }
-    }
-
-    test("Should validate params") {
-
-        when {
-
-            params {
-                monochrome_logs = true
-                test_data       = ''
-                outdir          = 1
-            }
-            workflow {
-                """
-                help             = false
-                workflow_command = null
-                pre_help_text    = null
-                post_help_text   = null
-                validate_params  = true
-                schema_filename  = "$moduleTestDir/nextflow_schema.json"
-
-                input[0] = help
-                input[1] = workflow_command
-                input[2] = pre_help_text
-                input[3] = post_help_text
-                input[4] = validate_params
-                input[5] = schema_filename
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.failed },
-                { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } }
-            )
-        }
-    }
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
deleted file mode 100644
index 60b1cfff4..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nfvalidation_plugin:
-  - subworkflows/nf-core/utils_nfvalidation_plugin/**
diff --git a/workflows/eager.nf b/workflows/eager.nf
index 0766744bd..64bdd8f9a 100644
--- a/workflows/eager.nf
+++ b/workflows/eager.nf
@@ -4,11 +4,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryMap         } from 'plugin/nf-validation'
-include { paramsSummaryMultiqc     } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText   } from '../subworkflows/local/utils_nfcore_eager_pipeline'
-include { addNewMetaFromAttributes } from '../subworkflows/local/utils_nfcore_eager_pipeline/main'
+include { paramsSummaryMap                                    } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc                                } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML                              } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText                              } from '../subworkflows/local/utils_nfcore_eager_pipeline'
+include { addNewMetaFromAttributes                            } from '../subworkflows/local/utils_nfcore_eager_pipeline/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -21,19 +21,19 @@ include { addNewMetaFromAttributes } from '../subworkflows/local/utils_nfcore_ea
 //
 
 // TODO rename to active: index_reference, filter_bam etc.
-include { REFERENCE_INDEXING                            } from '../subworkflows/local/reference_indexing'
-include { PREPROCESSING                                 } from '../subworkflows/local/preprocessing'
-include { MAP                                           } from '../subworkflows/local/map'
-include { FILTER_BAM                                    } from '../subworkflows/local/bamfiltering.nf'
-include { DEDUPLICATE                                   } from '../subworkflows/local/deduplicate'
-include { MANIPULATE_DAMAGE                             } from '../subworkflows/local/manipulate_damage'
-include { METAGENOMICS_COMPLEXITYFILTER                 } from '../subworkflows/local/metagenomics_complexityfilter'
-include { ESTIMATE_CONTAMINATION                        } from '../subworkflows/local/estimate_contamination'
-include { CALCULATE_DAMAGE                              } from '../subworkflows/local/calculate_damage'
-include { RUN_SEXDETERRMINE                             } from '../subworkflows/local/run_sex_determination'
-include { MERGE_LIBRARIES                               } from '../subworkflows/local/merge_libraries'
-include { MERGE_LIBRARIES as MERGE_LIBRARIES_GENOTYPING } from '../subworkflows/local/merge_libraries'
-include { GENOTYPE                                      } from '../subworkflows/local/genotype'
+include { REFERENCE_INDEXING                                  } from '../subworkflows/local/reference_indexing'
+include { PREPROCESSING                                       } from '../subworkflows/local/preprocessing'
+include { MAP                                                 } from '../subworkflows/local/map'
+include { FILTER_BAM                                          } from '../subworkflows/local/bamfiltering.nf'
+include { DEDUPLICATE                                         } from '../subworkflows/local/deduplicate'
+include { MANIPULATE_DAMAGE                                   } from '../subworkflows/local/manipulate_damage'
+include { METAGENOMICS_COMPLEXITYFILTER                       } from '../subworkflows/local/metagenomics_complexityfilter'
+include { ESTIMATE_CONTAMINATION                              } from '../subworkflows/local/estimate_contamination'
+include { CALCULATE_DAMAGE                                    } from '../subworkflows/local/calculate_damage'
+include { RUN_SEXDETERRMINE                                   } from '../subworkflows/local/run_sex_determination'
+include { MERGE_LIBRARIES                                     } from '../subworkflows/local/merge_libraries'
+include { MERGE_LIBRARIES as MERGE_LIBRARIES_GENOTYPING       } from '../subworkflows/local/merge_libraries'
+include { GENOTYPE                                            } from '../subworkflows/local/genotype'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -48,8 +48,8 @@ include { GENOTYPE                                      } from '../subworkflows/
 include { FASTQC                                              } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                                             } from '../modules/nf-core/multiqc/main'
 include { SAMTOOLS_COLLATEFASTQ as SAMTOOLS_CONVERT_BAM_INPUT } from '../modules/nf-core/samtools/collatefastq/main'
-include { CAT_FASTQ             as CAT_FASTQ_CONVERTED_BAM    } from '../modules/nf-core/cat/fastq/main'
-include { SAMTOOLS_INDEX        as SAMTOOLS_INDEX_BAM_INPUT   } from '../modules/nf-core/samtools/index/main'
+include { CAT_FASTQ as CAT_FASTQ_CONVERTED_BAM                } from '../modules/nf-core/cat/fastq/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAM_INPUT          } from '../modules/nf-core/samtools/index/main'
 include { PRESEQ_CCURVE                                       } from '../modules/nf-core/preseq/ccurve/main'
 include { PRESEQ_LCEXTRAP                                     } from '../modules/nf-core/preseq/lcextrap/main'
 include { FALCO                                               } from '../modules/nf-core/falco/main'
@@ -70,31 +70,33 @@ include { QUALIMAP_BAMQC as QUALIMAP_BAMQC_WITHBED            } from '../modules
 */
 
 workflow EAGER {
-
     take:
-    ch_samplesheet_fastqs // channel: samplesheet read in from --input
-    ch_samplesheet_bams
+    ch_samplesheet_fastqs // channel: samplesheet FASTQ entries read in from --input
+    ch_samplesheet_bams   // channel: samplesheet BAM entries read in from --input
 
     main:
 
-    log.info "Schaffa, Schaffa, Genome Baua!"
+    log.info("Schaffa, Schaffa, Genome Baua!")
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-
     // Reference
-    fasta_fn             = params.fasta ? file(params.fasta, checkIfExists: true) : params.fasta_sheet ? file(params.fasta_sheet, checkIfExists: true) : []
-    fasta_fai            = params.fasta_fai ? file(params.fasta_fai, checkIfExists: true) : []
-    fasta_dict           = params.fasta_dict ? file(params.fasta_dict, checkIfExists: true) : []
+    fasta_fn = params.fasta ? file(params.fasta, checkIfExists: true) : params.fasta_sheet ? file(params.fasta_sheet, checkIfExists: true) : []
+    fasta_fai = params.fasta_fai ? file(params.fasta_fai, checkIfExists: true) : []
+    fasta_dict = params.fasta_dict ? file(params.fasta_dict, checkIfExists: true) : []
     fasta_mapperindexdir = params.fasta_mapperindexdir ? file(params.fasta_mapperindexdir, checkIfExists: true) : []
 
     // Preprocessing
-    adapterlist          = params.preprocessing_skipadaptertrim ? [] : params.preprocessing_adapterlist ? file(params.preprocessing_adapterlist, checkIfExists: true) : []
+    adapterlist = params.preprocessing_skipadaptertrim ? [] : params.preprocessing_adapterlist ? file(params.preprocessing_adapterlist, checkIfExists: true) : []
 
-    if ( params.preprocessing_adapterlist                  && !params.preprocessing_skipadaptertrim ) {
-        if ( params.preprocessing_tool == 'adapterremoval' && !(adapterlist.extension == 'txt') ) error "[nf-core/eager] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}"
-        if ( params.preprocessing_tool == 'fastp'          && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)") ) error "[nf-core/eager] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}"
+    if (params.preprocessing_adapterlist && !params.preprocessing_skipadaptertrim) {
+        if (params.preprocessing_tool == 'adapterremoval' && !(adapterlist.extension == 'txt')) {
+            error("[nf-core/eager] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}")
+        }
+        if (params.preprocessing_tool == 'fastp' && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)")) {
+            error("[nf-core/eager] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}")
+        }
     }
 
     //
@@ -103,42 +105,36 @@ workflow EAGER {
 
     if (params.convert_inputbam) {
         // Convert input BAMs back to FastQ with non-interleaved output.
-        SAMTOOLS_CONVERT_BAM_INPUT ( ch_samplesheet_bams, [ [], [] ], false )
+        SAMTOOLS_CONVERT_BAM_INPUT(ch_samplesheet_bams, [[], []], false)
 
         // if BAM is single-end, pull R1 output as well as 'other' output and merge (in case collapsed reads have their R1 and R2 flags both set to 0 or 1)
         ch_single_end_reads = SAMTOOLS_CONVERT_BAM_INPUT.out.fastq
-            .filter {
-                meta, reads ->
+            .filter { meta, reads ->
                 meta.single_end
             }
             .join(SAMTOOLS_CONVERT_BAM_INPUT.out.fastq_other)
-            .map {
-                meta, read1, fastq_other ->
-                [meta, [read1, fastq_other] ]
+            .map { meta, read1, fastq_other ->
+                [meta, [read1, fastq_other]]
             }
 
         // Put all the converted FASTQs with single-end reads back together again
-        CAT_FASTQ_CONVERTED_BAM( ch_single_end_reads )
+        CAT_FASTQ_CONVERTED_BAM(ch_single_end_reads)
 
         //if BAM is paired-end, pull R1 and R2 outputs, discarding 'other' output and singletons
-        ch_paired_end_reads = SAMTOOLS_CONVERT_BAM_INPUT.out.fastq
-            .filter {
-                meta, reads ->
-                ! meta.single_end
-            }
+        ch_paired_end_reads = SAMTOOLS_CONVERT_BAM_INPUT.out.fastq.filter { meta, reads ->
+            !meta.single_end
+        }
 
         ch_fastqs_from_converted_bams = CAT_FASTQ_CONVERTED_BAM.out.reads
             .mix(ch_paired_end_reads)
-            // drop reference and id_index from meta
-            .map {
-                meta, reads ->
-                [ meta - meta.subMap('reference', 'id_index'), reads ]
+            .map { meta, reads ->
+                [meta - meta.subMap('reference', 'id_index'), reads]
             }
 
         // Mix the converted fastqs with the original fastqs
-        ch_fastqs_for_preprocessing = ch_fastqs_from_converted_bams
-            .mix( ch_samplesheet_fastqs )
-    } else {
+        ch_fastqs_for_preprocessing = ch_fastqs_from_converted_bams.mix(ch_samplesheet_fastqs)
+    }
+    else {
         // If BAM conversion is not activated , just use the original fastqs
         ch_fastqs_for_preprocessing = ch_samplesheet_fastqs
     }
@@ -147,74 +143,74 @@ workflow EAGER {
     // SUBWORKFLOW: Indexing of reference files
     //
 
-    REFERENCE_INDEXING ( fasta_fn, fasta_fai, fasta_dict, fasta_mapperindexdir )
-    ch_versions = ch_versions.mix( REFERENCE_INDEXING.out.versions )
+    REFERENCE_INDEXING(fasta_fn, fasta_fai, fasta_dict, fasta_mapperindexdir)
+    ch_versions = ch_versions.mix(REFERENCE_INDEXING.out.versions)
 
     //
     // MODULE: Run FastQC or Falco
     //
 
-    if ( params.sequencing_qc_tool == "falco" ) {
-        FALCO ( ch_fastqs_for_preprocessing )
-        ch_versions = ch_versions.mix( FALCO.out.versions.first() )
-        ch_multiqc_files = ch_multiqc_files.mix( FALCO.out.txt.collect{it[1]}.ifEmpty([]) )
-    } else {
-        FASTQC ( ch_fastqs_for_preprocessing )
-        ch_versions = ch_versions.mix( FASTQC.out.versions.first() )
-        ch_multiqc_files = ch_multiqc_files.mix( FASTQC.out.zip.collect{it[1]}.ifEmpty([]) )
+    if (params.sequencing_qc_tool == "falco") {
+        FALCO(ch_fastqs_for_preprocessing)
+        ch_versions = ch_versions.mix(FALCO.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(FALCO.out.txt.collect { it[1] }.ifEmpty([]))
+    }
+    else {
+        FASTQC(ch_fastqs_for_preprocessing)
+        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect { it[1] }.ifEmpty([]))
     }
 
     //
     // SUBWORKFLOW: Read preprocessing (clipping, merging, fastq trimming etc. )
     //
 
-    if ( !params.skip_preprocessing ) {
-        PREPROCESSING ( ch_fastqs_for_preprocessing, adapterlist )
+    if (!params.skip_preprocessing) {
+        PREPROCESSING(ch_fastqs_for_preprocessing, adapterlist)
         ch_reads_for_mapping = PREPROCESSING.out.reads
-        ch_versions          = ch_versions.mix( PREPROCESSING.out.versions )
-        ch_multiqc_files     = ch_multiqc_files.mix( PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
-    } else {
+        ch_versions = ch_versions.mix(PREPROCESSING.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(PREPROCESSING.out.mqc.collect { it[1] }.ifEmpty([]))
+    }
+    else {
         ch_reads_for_mapping = ch_fastqs_for_preprocessing
     }
 
     //
     // SUBWORKFLOW: Reference mapping
     //
-    ch_reference_for_mapping = REFERENCE_INDEXING.out.reference
-            .map{
-                meta, fasta, fai, dict, index ->
-                [ meta, index, fasta ]
-            }
+    ch_reference_for_mapping = REFERENCE_INDEXING.out.reference.map { meta, fasta, fai, dict, index ->
+        [meta, index, fasta]
+    }
 
-    MAP ( ch_reads_for_mapping, ch_reference_for_mapping, REFERENCE_INDEXING.out.elongated_reference, REFERENCE_INDEXING.out.elongated_chr_list )
+    MAP(ch_reads_for_mapping, ch_reference_for_mapping, REFERENCE_INDEXING.out.elongated_reference, REFERENCE_INDEXING.out.elongated_chr_list)
 
-    ch_versions       = ch_versions.mix( MAP.out.versions )
-    ch_multiqc_files  = ch_multiqc_files.mix( MAP.out.mqc.collect{it[1]}.ifEmpty([]) )
+    ch_versions = ch_versions.mix(MAP.out.versions)
+    ch_multiqc_files = ch_multiqc_files.mix(MAP.out.mqc.collect { it[1] }.ifEmpty([]))
 
     //
     //  MODULE: indexing of user supplied unconverted input BAMs
     //
 
-    if ( !params.convert_inputbam ){
-        SAMTOOLS_INDEX_BAM_INPUT ( ch_samplesheet_bams )
-        ch_versions = ch_versions.mix( SAMTOOLS_INDEX_BAM_INPUT.out.versions )
+    if (!params.convert_inputbam) {
+        SAMTOOLS_INDEX_BAM_INPUT(ch_samplesheet_bams)
+        ch_versions = ch_versions.mix(SAMTOOLS_INDEX_BAM_INPUT.out.versions)
 
-        if ( params.fasta_largeref ) {
-            ch_bams_from_input = ch_samplesheet_bams.join( SAMTOOLS_INDEX_BAM_INPUT.out.csi )
-        } else {
-            ch_bams_from_input = ch_samplesheet_bams.join( SAMTOOLS_INDEX_BAM_INPUT.out.bai )
+        if (params.fasta_largeref) {
+            ch_bams_from_input = ch_samplesheet_bams.join(SAMTOOLS_INDEX_BAM_INPUT.out.csi)
+        }
+        else {
+            ch_bams_from_input = ch_samplesheet_bams.join(SAMTOOLS_INDEX_BAM_INPUT.out.bai)
         }
 
         //
         // MODULE: flagstats of user supplied input BAMs
         //
-        SAMTOOLS_FLAGSTATS_BAM_INPUT ( ch_bams_from_input )
-        ch_versions           = ch_versions.mix( SAMTOOLS_FLAGSTATS_BAM_INPUT.out.versions )
-        ch_flagstat_input_bam = SAMTOOLS_FLAGSTATS_BAM_INPUT.out.flagstat // For endorspy
-
-
-    } else {
-        ch_bams_from_input    = Channel.empty()
+        SAMTOOLS_FLAGSTATS_BAM_INPUT(ch_bams_from_input)
+        ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTATS_BAM_INPUT.out.versions)
+        ch_flagstat_input_bam = SAMTOOLS_FLAGSTATS_BAM_INPUT.out.flagstat
+    }
+    else {
+        ch_bams_from_input = Channel.empty()
         ch_flagstat_input_bam = Channel.empty()
     }
 
@@ -222,22 +218,22 @@ workflow EAGER {
     // SUBWORKFLOW: bam filtering (length, mapped/unmapped, quality etc.)
     //
 
-    if ( params.run_bamfiltering || params.run_metagenomics ) {
+    if (params.run_bamfiltering || params.run_metagenomics) {
 
         ch_mapped_for_bamfilter = MAP.out.bam
-                                    .join(MAP.out.bai)
-                                    .mix(ch_bams_from_input)
+            .join(MAP.out.bai)
+            .mix(ch_bams_from_input)
 
-        FILTER_BAM ( ch_mapped_for_bamfilter )
+        FILTER_BAM(ch_mapped_for_bamfilter)
         ch_bamfiltered_for_deduplication = FILTER_BAM.out.genomics
-        ch_bamfiltered_for_metagenomics  = FILTER_BAM.out.metagenomics
-        ch_versions                      = ch_versions.mix( FILTER_BAM.out.versions )
-        ch_multiqc_files                 = ch_multiqc_files.mix( FILTER_BAM.out.mqc.collect{it[1]}.ifEmpty([]) )
-
-    } else {
+        ch_bamfiltered_for_metagenomics = FILTER_BAM.out.metagenomics
+        ch_versions = ch_versions.mix(FILTER_BAM.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(FILTER_BAM.out.mqc.collect { it[1] }.ifEmpty([]))
+    }
+    else {
         ch_bamfiltered_for_deduplication = MAP.out.bam
-                                                .join(MAP.out.bai)
-                                                .mix(ch_bams_from_input)
+            .join(MAP.out.bai)
+            .mix(ch_bams_from_input)
     }
 
     ch_reads_for_deduplication = ch_bamfiltered_for_deduplication
@@ -246,22 +242,19 @@ workflow EAGER {
     // SUBWORKFLOW: genomic BAM deduplication
     //
 
-    ch_fasta_for_deduplication = REFERENCE_INDEXING.out.reference
-        .multiMap{
-            meta, fasta, fai, dict, index ->
-            fasta:      [ meta, fasta ]
-            fasta_fai:  [ meta, fai ]
-        }
+    ch_fasta_for_deduplication = REFERENCE_INDEXING.out.reference.multiMap { meta, fasta, fai, dict, index ->
+        fasta: [meta, fasta]
+        fasta_fai: [meta, fai]
+    }
 
-    if ( !params.skip_deduplication ) {
-        DEDUPLICATE( ch_reads_for_deduplication, ch_fasta_for_deduplication.fasta, ch_fasta_for_deduplication.fasta_fai )
-        ch_dedupped_bams = DEDUPLICATE.out.bam
-            .join( DEDUPLICATE.out.bai )
+    if (!params.skip_deduplication) {
+        DEDUPLICATE(ch_reads_for_deduplication, ch_fasta_for_deduplication.fasta, ch_fasta_for_deduplication.fasta_fai)
+        ch_dedupped_bams = DEDUPLICATE.out.bam.join(DEDUPLICATE.out.bai)
         ch_dedupped_flagstat = DEDUPLICATE.out.flagstat
-        ch_versions                   = ch_versions.mix( DEDUPLICATE.out.versions )
-
-    } else {
-        ch_dedupped_bams     = ch_reads_for_deduplication
+        ch_versions = ch_versions.mix(DEDUPLICATE.out.versions)
+    }
+    else {
+        ch_dedupped_bams = ch_reads_for_deduplication
         ch_dedupped_flagstat = Channel.empty()
     }
 
@@ -269,96 +262,88 @@ workflow EAGER {
     // SUBWORKFLOW: Merge libraries per sample
     //
 
-    MERGE_LIBRARIES ( ch_dedupped_bams )
-    ch_versions          = ch_versions.mix( MERGE_LIBRARIES.out.versions )
+    MERGE_LIBRARIES(ch_dedupped_bams)
+    ch_versions = ch_versions.mix(MERGE_LIBRARIES.out.versions)
     ch_merged_dedup_bams = MERGE_LIBRARIES.out.bam_bai
-    ch_multiqc_files     = ch_multiqc_files.mix( MERGE_LIBRARIES.out.mqc.collect{it[1]}.ifEmpty([]) )
+    ch_multiqc_files = ch_multiqc_files.mix(MERGE_LIBRARIES.out.mqc.collect { it[1] }.ifEmpty([]))
 
     //
     // MODULE QUALIMAP
     //
 
-    if ( !params.skip_qualimap ) {
-        ch_snp_capture_bed = REFERENCE_INDEXING.out.snp_capture_bed
-            .map{
-                addNewMetaFromAttributes( it, "id" , "reference" , false )
-            }
+    if (!params.skip_qualimap) {
+        ch_snp_capture_bed = REFERENCE_INDEXING.out.snp_capture_bed.map {
+            addNewMetaFromAttributes(it, "id", "reference", false)
+        }
         ch_qualimap_input = ch_merged_dedup_bams
-            .map {
-            meta, bam, bai ->
-                [ meta, bam ]
+            .map { meta, bam, bai ->
+                [meta, bam]
             }
             .map {
-                addNewMetaFromAttributes( it, "reference" , "reference" , false )
+                addNewMetaFromAttributes(it, "reference", "reference", false)
             }
             .combine(
-                by: 0,
-                ch_snp_capture_bed
+                ch_snp_capture_bed,
+                by: 0
             )
-            .branch {
-                ignore_meta, meta, bam, meta2, snp_capture_bed ->
+            .branch { ignore_meta, meta, bam, meta2, snp_capture_bed ->
                 withbed: snp_capture_bed != ""
                 nobed: true
             }
-        ch_qualimap_input_with = ch_qualimap_input.withbed
-            .multiMap{
-                ignore_meta, meta, bam, meta2, snp_capture_bed ->
-                bam:             [ meta, bam ]
-                snp_capture_bed: [ snp_capture_bed ]
-            }
+        ch_qualimap_input_with = ch_qualimap_input.withbed.multiMap { ignore_meta, meta, bam, meta2, snp_capture_bed ->
+            bam: [meta, bam]
+            snp_capture_bed: [snp_capture_bed]
+        }
 
-        QUALIMAP_BAMQC_WITHBED( ch_qualimap_input_with.bam, ch_qualimap_input_with.snp_capture_bed )
-        ch_qualimap_input_without = ch_qualimap_input.nobed
-            .map{
-                ignore_meta, meta, bam, meta2, snp_capture_bed ->
-                [ meta, bam ]
-            }
+        QUALIMAP_BAMQC_WITHBED(ch_qualimap_input_with.bam, ch_qualimap_input_with.snp_capture_bed)
+        ch_qualimap_input_without = ch_qualimap_input.nobed.map { ignore_meta, meta, bam, meta2, snp_capture_bed ->
+            [meta, bam]
+        }
 
-        QUALIMAP_BAMQC_NOBED( ch_qualimap_input_without, [] )
-        ch_qualimap_output = QUALIMAP_BAMQC_WITHBED.out.results.mix( QUALIMAP_BAMQC_NOBED.out.results )
-        ch_versions = ch_versions.mix( QUALIMAP_BAMQC_NOBED.out.versions ).mix( QUALIMAP_BAMQC_WITHBED.out.versions )
+        QUALIMAP_BAMQC_NOBED(ch_qualimap_input_without, [])
+        ch_qualimap_output = QUALIMAP_BAMQC_WITHBED.out.results.mix(QUALIMAP_BAMQC_NOBED.out.results)
+        ch_versions = ch_versions.mix(QUALIMAP_BAMQC_NOBED.out.versions).mix(QUALIMAP_BAMQC_WITHBED.out.versions)
     }
 
     //
     // MODULE: remove reads mapping to the host from the raw fastq
     //
 
-    if ( params.run_host_removal ) {
+    if (params.run_host_removal) {
         // Preparing bam channel for host removal to be combined with the input fastq channel
         // The bam channel consist of [meta, bam, bai] and in the meta we have in addition 'single_end' always set as TRUE and 'reference' set
         // To be able to join it with fastq channel, we need to remove them from the meta (done in map) and stored in new_meta
-        ch_bam_for_host_removal= MAP.out.bam.join(MAP.out.bai)
-                                            .map{
-                                                meta, bam, bai ->
-                                                new_meta = meta.clone().findAll{ it.key !in [ 'single_end', 'reference' ] }
-                                                [ new_meta, meta, bam, bai ]
-                                                }
+        ch_bam_for_host_removal = MAP.out.bam
+            .join(MAP.out.bai)
+            .map { meta, bam, bai ->
+                new_meta = meta.clone().findAll { it.key !in ['single_end', 'reference'] }
+                [new_meta, meta, bam, bai]
+            }
         // Preparing fastq channel for host removal to be combined with the bam channel
         // The meta of the fastq channel contains additional fields when compared to the meta from the bam channel: lane, colour_chemistry,
         // and not necessarily matching single_end. Those fields are dropped of the meta in the map and stored in new_meta
-        ch_fastqs_for_host_removal= ch_fastqs_for_preprocessing.map{
-                                                        meta, fastqs ->
-                                                        new_meta = meta.clone().findAll{ it.key !in [ 'lane', 'colour_chemistry', 'single_end' ] }
-                                                        [ new_meta, meta, fastqs ]
-                                                    }
+        ch_fastqs_for_host_removal = ch_fastqs_for_preprocessing.map { meta, fastqs ->
+            new_meta = meta.clone().findAll { it.key !in ['lane', 'colour_chemistry', 'single_end'] }
+            [new_meta, meta, fastqs]
+        }
         // We join the bam and fastq channel with now matching metas (new_meta) referred as meta_join
         // and remove the meta_join from the final channel, keeping the original metas for the bam and the fastqs
-        ch_input_for_host_removal = ch_bam_for_host_removal.join(ch_fastqs_for_host_removal)
-                                                    .map{
-                                                        meta_join, meta_bam, bam, bai, meta_fastq, fastqs ->
-                                                        [ meta_bam, bam, bai, meta_fastq, fastqs]
-                                                    }
+        ch_input_for_host_removal = ch_bam_for_host_removal
+            .join(ch_fastqs_for_host_removal)
+            .map { meta_join, meta_bam, bam, bai, meta_fastq, fastqs ->
+                [meta_bam, bam, bai, meta_fastq, fastqs]
+            }
 
-        HOST_REMOVAL ( ch_input_for_host_removal )
+        HOST_REMOVAL(ch_input_for_host_removal)
 
-        ch_versions = ch_versions.mix( HOST_REMOVAL.out.versions )
+        ch_versions = ch_versions.mix(HOST_REMOVAL.out.versions)
     }
 
     //
     // Section: Metagenomics
     //
 
-    if ( params.run_metagenomics ) {
+    if (params.run_metagenomics) {
 
         ch_database = Channel.fromPath(params.metagenomics_profiling_database)
 
@@ -366,94 +351,93 @@ workflow EAGER {
         ch_tax_list = Channel.empty()
         ch_ncbi_dir = Channel.empty()
 
-        if ( params.metagenomics_run_postprocessing && params.metagenomics_profiling_tool == 'malt' ){
-            ch_tax_list = Channel.fromPath(params.metagenomics_maltextract_taxonlist, checkIfExists:true)
-            ch_ncbi_dir = Channel.fromPath(params.metagenomics_maltextract_ncbidir, checkIfExists:true)
+        if (params.metagenomics_run_postprocessing && params.metagenomics_profiling_tool == 'malt') {
+            ch_tax_list = Channel.fromPath(params.metagenomics_maltextract_taxonlist, checkIfExists: true)
+            ch_ncbi_dir = Channel.fromPath(params.metagenomics_maltextract_ncbidir, checkIfExists: true)
         }
 
-        METAGENOMICS ( ch_bamfiltered_for_metagenomics, ch_database, ch_tax_list, ch_ncbi_dir )
-        ch_versions      = ch_versions.mix( METAGENOMICS.out.versions.first() )
-        ch_multiqc_files = ch_multiqc_files.mix( METAGENOMICS.out.ch_multiqc_files )
+        METAGENOMICS(ch_bamfiltered_for_metagenomics, ch_database, ch_tax_list, ch_ncbi_dir)
+        ch_versions = ch_versions.mix(METAGENOMICS.out.versions.first())
+        ch_multiqc_files = ch_multiqc_files.mix(METAGENOMICS.out.ch_multiqc_files)
     }
 
     //
     // MODULE: MTNUCRATIO
     //
 
-    if ( params.run_mtnucratio ) {
-        ch_mito_header = REFERENCE_INDEXING.out.mitochondrion_header
-            .map{
-                addNewMetaFromAttributes( it, "id" , "reference" , false )
-            }
+    if (params.run_mtnucratio) {
+        ch_mito_header = REFERENCE_INDEXING.out.mitochondrion_header.map {
+            addNewMetaFromAttributes(it, "id", "reference", false)
+        }
         mtnucratio_input = ch_dedupped_bams
             .map {
-                addNewMetaFromAttributes( it, "reference" , "reference" , false )
+                addNewMetaFromAttributes(it, "reference", "reference", false)
             }
             .combine(
-                by: 0,
-                ch_mito_header
+                ch_mito_header,
+                by: 0
             )
-            .multiMap{
-                ignore_meta, meta, bam, bai, meta2, mito_header ->
-                bam:         [ meta, bam ]
-                mito_header: [ meta2, mito_header ]
+            .multiMap { ignore_meta, meta, bam, bai, meta2, mito_header ->
+                bam: [meta, bam]
+                mito_header: [meta2, mito_header]
             }
 
-        MTNUCRATIO( mtnucratio_input.bam, mtnucratio_input.mito_header.map{ it[1] } )
-        ch_multiqc_files = ch_multiqc_files.mix(MTNUCRATIO.out.mtnucratio.collect{it[1]}.ifEmpty([]))
-        ch_versions      = ch_versions.mix( MTNUCRATIO.out.versions )
+        MTNUCRATIO(mtnucratio_input.bam, mtnucratio_input.mito_header.map { it[1] })
+        ch_multiqc_files = ch_multiqc_files.mix(MTNUCRATIO.out.mtnucratio.collect { it[1] }.ifEmpty([]))
+        ch_versions = ch_versions.mix(MTNUCRATIO.out.versions)
     }
 
     //
     // MODULE: ENDORSPY (raw, filtered, deduplicated)
     //
 
-    ch_flagstat_for_endorspy_raw    = MAP.out.flagstat
-                                            .mix( ch_flagstat_input_bam )
+    ch_flagstat_for_endorspy_raw = MAP.out.flagstat.mix(ch_flagstat_input_bam)
 
-    if ( params.run_bamfiltering & !params.skip_deduplication ) {
-        ch_for_endorspy = ch_flagstat_for_endorspy_raw
-                                                .join (FILTER_BAM.out.flagstat)
-                                                .join (DEDUPLICATE.out.flagstat)
-    } else if ( params.run_bamfiltering & params.skip_deduplication ) {
+    if (params.run_bamfiltering & !params.skip_deduplication) {
         ch_for_endorspy = ch_flagstat_for_endorspy_raw
-                                                        .join (FILTER_BAM.out.flagstat)
-                                                        .map{
-                                                            meta, flags_raw, flags_filtered ->
-                                                            [ meta, flags_raw, flags_filtered, [] ]
-                                                            }
-    } else if ( !params.run_bamfiltering & !params.skip_deduplication) {
+            .join(FILTER_BAM.out.flagstat)
+            .join(DEDUPLICATE.out.flagstat)
+    }
+    else if (params.run_bamfiltering & params.skip_deduplication) {
         ch_for_endorspy = ch_flagstat_for_endorspy_raw
-                                                        .join (DEDUPLICATE.out.flagstat)
-                                                        . map{
-                                                            meta, flags_raw, flags_dedup ->
-                                                            [ meta, flags_raw, [], flags_dedup ]
-                                                            }
-    } else {
+            .join(FILTER_BAM.out.flagstat)
+            .map { meta, flags_raw, flags_filtered ->
+                [meta, flags_raw, flags_filtered, []]
+            }
+    }
+    else if (!params.run_bamfiltering & !params.skip_deduplication) {
         ch_for_endorspy = ch_flagstat_for_endorspy_raw
-                                                        .map {
-                                                            meta, flags_raw ->
-                                                            [ meta, flags_raw, [], [] ]
-                                                        }
+            .join(DEDUPLICATE.out.flagstat)
+            .map { meta, flags_raw, flags_dedup ->
+                [meta, flags_raw, [], flags_dedup]
+            }
+    }
+    else {
+        ch_for_endorspy = ch_flagstat_for_endorspy_raw.map { meta, flags_raw ->
+            [meta, flags_raw, [], []]
+        }
     }
 
-    ENDORSPY ( ch_for_endorspy )
+    ENDORSPY(ch_for_endorspy)
 
-    ch_versions       = ch_versions.mix( ENDORSPY.out.versions )
-    ch_multiqc_files  = ch_multiqc_files.mix( ENDORSPY.out.json.collect{it[1]}.ifEmpty([]) )
+    ch_versions = ch_versions.mix(ENDORSPY.out.versions)
+    ch_multiqc_files = ch_multiqc_files.mix(ENDORSPY.out.json.collect { it[1] }.ifEmpty([]))
 
     //
     // MODULE: PreSeq
     //
 
-    if ( !params.mapstats_skip_preseq && params.mapstats_preseq_mode == 'c_curve') {
-        PRESEQ_CCURVE(ch_reads_for_deduplication.map{[it[0],it[1]]})
-        ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_CCURVE.out.c_curve.collect{it[1]}.ifEmpty([]))
-        ch_versions = ch_versions.mix( PRESEQ_CCURVE.out.versions )
-    } else ( !params.mapstats_skip_preseq && params.mapstats_preseq_mode == 'lc_extrap') {
-        PRESEQ_LCEXTRAP(ch_reads_for_deduplication.map{[it[0],it[1]]})
-        ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.lc_extrap.collect{it[1]}.ifEmpty([]))
-        ch_versions = ch_versions.mix( PRESEQ_LCEXTRAP.out.versions )
+    if (!params.mapstats_skip_preseq && params.mapstats_preseq_mode == 'c_curve') {
+        PRESEQ_CCURVE(ch_reads_for_deduplication.map { [it[0], it[1]] })
+        ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_CCURVE.out.c_curve.collect { it[1] }.ifEmpty([]))
+        ch_versions = ch_versions.mix(PRESEQ_CCURVE.out.versions)
+    }
+    else {
+        (!params.mapstats_skip_preseq && params.mapstats_preseq_mode == 'lc_extrap').call {
+            PRESEQ_LCEXTRAP(ch_reads_for_deduplication.map { [it[0], it[1]] })
+            ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.lc_extrap.collect { it[1] }.ifEmpty([]))
+            ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions)
+        }
     }
 
 
@@ -461,108 +445,101 @@ workflow EAGER {
     // MODULE: Bedtools coverage
     //
 
-    if ( params.run_bedtools_coverage ) {
+    if (params.run_bedtools_coverage) {
 
-        ch_bedtools_feature = REFERENCE_INDEXING.out.bedtools_feature
-                                .map{
-                                    addNewMetaFromAttributes( it, "id" , "reference" , false )
-                                }
+        ch_bedtools_feature = REFERENCE_INDEXING.out.bedtools_feature.map {
+            addNewMetaFromAttributes(it, "id", "reference", false)
+        }
 
         ch_bedtools_prep = ch_merged_dedup_bams
-                    .map {
-                        addNewMetaFromAttributes( it, "reference" , "reference" , false )
-                    }
-                    .combine(
-                        by: 0,
-                        ch_bedtools_feature
-                    )
-                    .map{
-                        ignore_meta, meta, bam, bai, meta2, bedtools_feature ->
-                        [ meta, bedtools_feature, bam, bai ]
-                    }
-                    .branch{
-                        meta, bedtools_feature, bam, bai ->
-                        withfeature: bedtools_feature != ""
-                        nobed: true
-                    }
+            .map {
+                addNewMetaFromAttributes(it, "reference", "reference", false)
+            }
+            .combine(
+                ch_bedtools_feature,
+                by: 0
+            )
+            .map { ignore_meta, meta, bam, bai, meta2, bedtools_feature ->
+                [meta, bedtools_feature, bam, bai]
+            }
+            .branch { meta, bedtools_feature, bam, bai ->
+                withfeature: bedtools_feature != ""
+                nobed: true
+            }
 
         // Running samtools view to get header
-        ch_bedtools_input = ch_bedtools_prep.withfeature
-                        .multiMap{
-                            meta, bedtools_feature, bam, bai ->
-                            bam: [ meta, bam, bai ]
-                            withfeature: [ meta, bedtools_feature, bam ]
-                        }
+        ch_bedtools_input = ch_bedtools_prep.withfeature.multiMap { meta, bedtools_feature, bam, bai ->
+            bam: [meta, bam, bai]
+            withfeature: [meta, bedtools_feature, bam]
+        }
 
-        SAMTOOLS_VIEW_GENOME( ch_bedtools_input.bam )
+        SAMTOOLS_VIEW_GENOME(ch_bedtools_input.bam)
 
         ch_genome_for_bedtools = SAMTOOLS_VIEW_GENOME.out.genome
 
         BEDTOOLS_COVERAGE_DEPTH(ch_bedtools_input.withfeature, ch_genome_for_bedtools)
 
-        ch_versions = ch_versions.mix( SAMTOOLS_VIEW_GENOME.out.versions )
+        ch_versions = ch_versions.mix(SAMTOOLS_VIEW_GENOME.out.versions)
         //ch_versions = ch_versions.mix( BEDTOOLS_COVERAGE_BREADTH.out.versions )
-        ch_versions = ch_versions.mix( BEDTOOLS_COVERAGE_DEPTH.out.versions )
+        ch_versions = ch_versions.mix(BEDTOOLS_COVERAGE_DEPTH.out.versions)
     }
 
     //
     // SUBWORKFLOW: Calculate Damage
     //
 
-    ch_fasta_for_damagecalculation = REFERENCE_INDEXING.out.reference
-        .multiMap{
-            meta, fasta, fai, dict, index ->
-            fasta:      [ meta, fasta ]
-            fasta_fai:  [ meta, fai ]
-        }
-
-    if ( !params.skip_damagecalculation ) {
-        CALCULATE_DAMAGE( ch_dedupped_bams, ch_fasta_for_damagecalculation.fasta, ch_fasta_for_damagecalculation.fasta_fai )
-        ch_versions      = ch_versions.mix( CALCULATE_DAMAGE.out.versions )
-        ch_multiqc_files = ch_multiqc_files.mix(CALCULATE_DAMAGE.out.mqc.collect{it[1]}.ifEmpty([]))
+    ch_fasta_for_damagecalculation = REFERENCE_INDEXING.out.reference.multiMap { meta, fasta, fai, dict, index ->
+        fasta: [meta, fasta]
+        fasta_fai: [meta, fai]
+    }
 
+    if (!params.skip_damagecalculation) {
+        CALCULATE_DAMAGE(ch_dedupped_bams, ch_fasta_for_damagecalculation.fasta, ch_fasta_for_damagecalculation.fasta_fai)
+        ch_versions = ch_versions.mix(CALCULATE_DAMAGE.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(CALCULATE_DAMAGE.out.mqc.collect { it[1] }.ifEmpty([]))
     }
 
     //
     // SUBWORKFLOW: Run Sex Determination
     //
 
-    if ( params.run_sexdeterrmine ) {
+    if (params.run_sexdeterrmine) {
         ch_sexdeterrmine_input = ch_merged_dedup_bams
 
-        RUN_SEXDETERRMINE(ch_sexdeterrmine_input, REFERENCE_INDEXING.out.sexdeterrmine_bed )
-        ch_versions      = ch_versions.mix( RUN_SEXDETERRMINE.out.versions )
-        ch_multiqc_files = ch_multiqc_files.mix( RUN_SEXDETERRMINE.out.mqc.collect{it[1]}.ifEmpty([]) )
+        RUN_SEXDETERRMINE(ch_sexdeterrmine_input, REFERENCE_INDEXING.out.sexdeterrmine_bed)
+        ch_versions = ch_versions.mix(RUN_SEXDETERRMINE.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(RUN_SEXDETERRMINE.out.mqc.collect { it[1] }.ifEmpty([]))
     }
 
     //
     // SUBWORKFLOW: Contamination estimation
     //
 
-    if ( params.run_contamination_estimation_angsd ) {
+    if (params.run_contamination_estimation_angsd) {
         contamination_input = ch_dedupped_bams
 
-        ESTIMATE_CONTAMINATION( contamination_input, REFERENCE_INDEXING.out.hapmap )
-        ch_versions      = ch_versions.mix( ESTIMATE_CONTAMINATION.out.versions )
-        ch_multiqc_files = ch_multiqc_files.mix( ESTIMATE_CONTAMINATION.out.mqc.collect{it[1]}.ifEmpty([]) )
+        ESTIMATE_CONTAMINATION(contamination_input, REFERENCE_INDEXING.out.hapmap)
+        ch_versions = ch_versions.mix(ESTIMATE_CONTAMINATION.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(ESTIMATE_CONTAMINATION.out.mqc.collect { it[1] }.ifEmpty([]))
     }
 
     //
     // SUBWORKFLOW: aDNA Damage Manipulation
     //
 
-    if ( params.run_mapdamage_rescaling || params.run_pmd_filtering || params.run_trim_bam ) {
-        MANIPULATE_DAMAGE( ch_dedupped_bams, ch_fasta_for_deduplication.fasta, REFERENCE_INDEXING.out.pmd_masking )
-        ch_multiqc_files          = ch_multiqc_files.mix( MANIPULATE_DAMAGE.out.flagstat.collect{it[1]}.ifEmpty([]) )
-        ch_versions               = ch_versions.mix( MANIPULATE_DAMAGE.out.versions )
+    if (params.run_mapdamage_rescaling || params.run_pmd_filtering || params.run_trim_bam) {
+        MANIPULATE_DAMAGE(ch_dedupped_bams, ch_fasta_for_deduplication.fasta, REFERENCE_INDEXING.out.pmd_masking)
+        ch_multiqc_files = ch_multiqc_files.mix(MANIPULATE_DAMAGE.out.flagstat.collect { it[1] }.ifEmpty([]))
+        ch_versions = ch_versions.mix(MANIPULATE_DAMAGE.out.versions)
         ch_bams_for_library_merge = params.genotyping_source == 'rescaled' ? MANIPULATE_DAMAGE.out.rescaled : params.genotyping_source == 'pmd' ? MANIPULATE_DAMAGE.out.filtered : params.genotyping_source == 'trimmed' ? MANIPULATE_DAMAGE.out.trimmed : ch_merged_dedup_bams
 
-    // SUBWORKFLOW: merge libraries for genotyping
-        MERGE_LIBRARIES_GENOTYPING ( ch_bams_for_library_merge )
-        ch_versions            = ch_versions.mix( MERGE_LIBRARIES_GENOTYPING.out.versions )
+        // SUBWORKFLOW: merge libraries for genotyping
+        MERGE_LIBRARIES_GENOTYPING(ch_bams_for_library_merge)
+        ch_versions = ch_versions.mix(MERGE_LIBRARIES_GENOTYPING.out.versions)
         ch_bams_for_genotyping = MERGE_LIBRARIES_GENOTYPING.out.bam_bai
-        ch_multiqc_files       = ch_multiqc_files.mix( MERGE_LIBRARIES_GENOTYPING.out.mqc.collect{it[1]}.ifEmpty([]) )
-    } else {
+        ch_multiqc_files = ch_multiqc_files.mix(MERGE_LIBRARIES_GENOTYPING.out.mqc.collect { it[1] }.ifEmpty([]))
+    }
+    else {
         ch_bams_for_genotyping = ch_merged_dedup_bams
     }
 
@@ -570,22 +547,19 @@ workflow EAGER {
     // SUBWORKFLOW: Genotyping
     //
 
-    if ( params.run_genotyping ) {
-        ch_reference_for_genotyping = REFERENCE_INDEXING.out.reference
-            // Remove unnecessary files from the reference channel, so SWF doesn't break with each change to reference channel.
-            .map {
-                meta, fasta, fai, dict, mapindex ->
-                [ meta, fasta, fai, dict ]
-            }
+    if (params.run_genotyping) {
+        ch_reference_for_genotyping = REFERENCE_INDEXING.out.reference.map { meta, fasta, fai, dict, mapindex ->
+            [meta, fasta, fai, dict]
+        }
         GENOTYPE(
-                ch_bams_for_genotyping, // [ [meta] , bam, bai ]
-                ch_reference_for_genotyping, // [ [ref_meta] , fasta, fai, dict ]
-                REFERENCE_INDEXING.out.pileupcaller_bed_snp.ifEmpty([[],[],[]]), // [ [ref_meta] , bed, snp ]
-                REFERENCE_INDEXING.out.dbsnp.ifEmpty([[],[]]) // [ [ref_meta] , dbsnp ]
-            )
+            ch_bams_for_genotyping,
+            ch_reference_for_genotyping,
+            REFERENCE_INDEXING.out.pileupcaller_bed_snp.ifEmpty([[], [], []]),
+            REFERENCE_INDEXING.out.dbsnp.ifEmpty([[], []])
+        )
 
-        ch_versions      = ch_versions.mix( GENOTYPE.out.versions )
-        ch_multiqc_files = ch_multiqc_files.mix( GENOTYPE.out.mqc.collect{it[1]}.ifEmpty([]) )
+        ch_versions = ch_versions.mix(GENOTYPE.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(GENOTYPE.out.mqc.collect { it[1] }.ifEmpty([]))
     }
 
     //
@@ -594,35 +568,42 @@ workflow EAGER {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml',
             sort: true,
             newLine: true
-        ).set { ch_collated_versions }
+        )
+        .set { ch_collated_versions }
+
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
-        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
-    ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
-
-    summary_params      = paramsSummaryMap(
-        workflow, parameters_schema: "nextflow_schema.json")
+    ch_multiqc_config = Channel.fromPath(
+        "${projectDir}/assets/multiqc_config.yml",
+        checkIfExists: true
+    )
+    ch_multiqc_custom_config = params.multiqc_config
+        ? Channel.fromPath(params.multiqc_config, checkIfExists: true)
+        : Channel.empty()
+    ch_multiqc_logo = params.multiqc_logo
+        ? Channel.fromPath(params.multiqc_logo, checkIfExists: true)
+        : Channel.empty()
+
+    summary_params = paramsSummaryMap(
+        workflow,
+        parameters_schema: "nextflow_schema.json"
+    )
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
-        file(params.multiqc_methods_description, checkIfExists: true) :
-        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
-        methodsDescriptionText(ch_multiqc_custom_methods_description))
-
     ch_multiqc_files = ch_multiqc_files.mix(
-        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
+    )
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description
+        ? file(params.multiqc_methods_description, checkIfExists: true)
+        : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description)
+    )
+
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
@@ -631,24 +612,20 @@ workflow EAGER {
         )
     )
 
-    if ( !params.skip_qualimap ) {
-        ch_multiqc_files = ch_multiqc_files.mix( ch_qualimap_output.collect{it[1]}.ifEmpty([]) )
+    if (!params.skip_qualimap) {
+        ch_multiqc_files = ch_multiqc_files.mix(ch_qualimap_output.collect { it[1] }.ifEmpty([]))
     }
 
-    MULTIQC (
+    MULTIQC(
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 
     emit:
     multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
-    versions       = ch_versions                 // channel: [ path(versions.yml) ]
+    versions       = ch_versions // channel: [ path(versions.yml) ]
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/