diff --git a/.editorconfig b/.editorconfig
index 72dda289..6d9b74cc 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 4355e2dd..1da1277a 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/taxprofiler: Contributing Guidelines
+# `nf-core/taxprofiler`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/taxprofiler.
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/taxprofiler, the standard workflow
 1. Check that there isn't already an issue about your idea in the [nf-core/taxprofiler issues](https://github.com/nf-core/taxprofiler/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/taxprofiler repository](https://github.com/nf-core/taxprofiler) 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.
 
@@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
@@ -65,17 +65,17 @@ For further information/help, please consult the [nf-core/taxprofiler documentat
 
 ## Pipeline contribution conventions
 
-To make the nf-core/taxprofiler code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/taxprofiler` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 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`.
@@ -84,13 +84,13 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
-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/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 61971716..48e71762 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -9,7 +9,6 @@ body:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
         - [nf-core/taxprofiler pipeline documentation](https://nf-co.re/taxprofiler/usage)
-
   - type: textarea
     id: description
     attributes:
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 69a2dd8e..4cbdf7a5 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/taxp
 - [ ] 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/taxprofiler/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/taxprofiler _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 bc40e7e3..76255088 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,18 +1,48 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the main/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:
+      - main
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/taxprofiler'
+    # 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/taxprofiler' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
+        if: github.event_name != 'workflow_dispatch'
+        id: check_approvals
+        continue-on-error: true
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ 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
         with:
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index e5e57686..ef90ee78 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/taxprofiler'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6c95a2b3..8ec3783c 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 }}"
@@ -17,7 +20,7 @@ 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/taxprofiler') }}"
     runs-on: ubuntu-latest
@@ -25,9 +28,13 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
-        tags:
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
           - "test"
           - "test_nopreprocessing"
           - "test_noprofiling"
@@ -39,37 +46,63 @@ jobs:
           - "test_alternativepreprocessing"
           - "test_bbduk"
           - "test_prinseqplusplus"
-
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - 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: 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: |
-          sudo locale-gen en_US.UTF-8
-          sudo update-locale LANG=en_US.UTF-8
+          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
         run: |
-          if [[ "${{ matrix.tags }}" == "test_motus" ]]; then
+          if [[ "${{ matrix.test_name }}" == "test_motus" ]]; then
             wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
             python downloadDB.py --no-download-progress
             echo 'tool,db_name,db_params,db_type,db_path' > 'database_motus.csv'
             echo "motus,db1_mOTU,,short,db_mOTU" >> 'database_motus.csv'
             echo "motus,db2_mOTU,,long,db_mOTU" >> 'database_motus.csv'
             echo "motus,db3_mOTU,,short;long,db_mOTU" >> 'database_motus.csv'
-            nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }};
+            nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},${{ matrix.test_name }} --databases ./database_motus.csv --outdir ./results_${{ matrix.test_name }};
           else
-            nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --outdir ./results_${{ matrix.tags }};
+            nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},${{ matrix.test_name }} --outdir ./results_${{ matrix.test_name }};
           fi
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d644..ab06316e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,14 +1,14 @@
-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
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 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:
@@ -17,17 +17,34 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
   NXF_ANSI_LOG: false
 
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
   download:
     runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -35,52 +52,83 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         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: |
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
+      - name: Make a cache directory for the container images
         run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+          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 }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.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/library/" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
+
+      - 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_OUTPUT"
 
       - 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' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.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() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
+            difference=$((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 > ./container_afterwards
+            diff ./container_initial ./container_afterwards
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 7a068de2..734d22ce 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe88..dbd52d5a 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:
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,27 +31,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           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() }}
@@ -59,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f..95b6b6af 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 03ecfcf7..76a9e67e 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(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:
@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 00000000..537529bc
--- /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@11bd71901bbe5b1630ceea73d27597364c9af683 # 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 5124c9ac..a42ce016 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/
diff --git a/.gitpod.yml b/.gitpod.yml
index 105a1821..83599f63 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,7 @@ 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
-    - 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
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index e0b85a77..18ad21e4 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,2 +1,15 @@
+nf_core_version: 3.2.0
 repository_type: pipeline
-nf_core_version: "2.14.1"
+template:
+  author: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li,
+    and the nf-core/taxprofiler team
+  description: Taxonomic classification and profiling of shotgun short- and long-read
+    metagenomic data
+  force: false
+  is_nfcore: true
+  name: taxprofiler
+  org: nf-core
+  outdir: .
+  skip_features:
+    - igenomes
+  version: 1.3.0dev
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1dc..1dec8650 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: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/.prettierignore b/.prettierignore
index abb4b4d6..f6400d75 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -10,4 +10,5 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json
 tests/
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 00000000..a33b527c
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49c10a61..4ce74cc0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,42 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [573](https://github.com/nf-core/taxprofiler/pull/573) Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+### `Deprecated`
+
+## v1.2.2 - Bouncy Basenji Patch [2024-01-15]
+
+### `Added`
+
+- [#558](https://github.com/nf-core/taxprofiler/pull/558) Updated to nf-core pipeline template v3.1.0 (added by @LilyAnderssonLee)
+- [#565](https://github.com/nf-core/taxprofiler/pull/565) Updated to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)
+
+### `Fixed`
+
+- [#561](https://github.com/nf-core/taxprofiler/pull/561) Updated Centrifuge to fix internal error when running with conda (❤️ to @AnotherSimon for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+| Tool       | Previous version | New version |
+| ---------- | ---------------- | ----------- |
+| centrifuge | 1.0.4.1          | 1.0.4.2     |
+
+### `Deprecated`
+
+## v1.2.1 - Bouncy Basenji Patch [2024-11-28]
+
+### `Added`
+
+- [#545](https://github.com/nf-core/taxprofiler/pull/545) Updated to nf-core pipeline template v3.0.2 (added by @LilyAnderssonLee & @jfy133)
+
+### `Fixed`
+
+- [#550](https://github.com/nf-core/taxprofiler/pull/550/) Fixed a bug where single-end data with the same sample names that include `.` in it would overwrite output files (❤️ to @SannaAb for reporting, fixed by @Midnighter)
+- [#552](https://github.com/nf-core/taxprofiler/pull/552) Fixed the issue where nonpareil fails due to insufficient data for calculation caused by a missing PNG (❤️ to @Joon-Klaps for reporting, fixed by @LilyAnderssonLee)
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/LICENSE b/LICENSE
index 694c9953..4eea3e9d 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team
+Copyright (c) The nf-core/taxprofiler team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 5999cf12..dafcd31d 100644
--- a/README.md
+++ b/README.md
@@ -7,9 +7,10 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364)
+
 [![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/)
@@ -93,8 +94,7 @@ nextflow run nf-core/taxprofiler \
 ```
 
 > [!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/taxprofiler/usage) and the [parameter documentation](https://nf-co.re/taxprofiler/parameters).
 
@@ -106,13 +106,14 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team.
+nf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team.
 
 ### Team
 
 - [James A. Fellows Yates](https://github.com/jfy133)
 - [Sofia Stamouli](https://github.com/sofstam)
 - [Moritz E. Beber](https://github.com/Midnighter)
+- [Lili Andersson-Li](https://github.com/LilyAnderssonLee)
 
 We thank the following people for their contributions to the development of this pipeline:
 
@@ -123,7 +124,6 @@ We thank the following people for their contributions to the development of this
 - [Jianhong Ou](https://github.com/jianhong)
 - [Rafal Stepien](https://github.com/rafalstepien)
 - [Mahwash Jamy](https://github.com/mjamy)
-- [Lily Andersson Lee](https://github.com/LilyAnderssonLee)
 
 ### Acknowledgments
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index ddcd7d9e..e4628504 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,9 +1,8 @@
 report_comment: >
-
-  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/tree/dev" target="_blank">nf-core/taxprofiler</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/taxprofiler/dev/docs/output" target="_blank">documentation</a>.
-
+  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/tree/dev"
+  target="_blank">nf-core/taxprofiler</a> analysis pipeline. For information about
+  how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/dev/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-taxprofiler-methods-description":
     order: -1000
@@ -100,14 +99,18 @@ top_modules:
         - "*raw*"
       path_filters_exclude:
         - "*processed*"
-      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+      extra: |
+        If used in this run, Falco is a drop-in replacement for FastQC producing
+        the same output, written by Guilherme de Sena Brandine and Andrew D. Smith.
   - "fastqc":
       name: "FastQC / Falco (post-Trimming)"
       path_filters:
         - "*processed*"
       path_filters_exclude:
         - "*raw*"
-      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+      extra: |
+        If used in this run, Falco is a drop-in replacement for FastQC producing
+        the same output, written by Guilherme de Sena Brandine and Andrew D. Smith.
   - nonpareil
   - "porechop":
       name: "Porechop"
@@ -115,7 +118,10 @@ top_modules:
       target: "Porechop"
       path_filters:
         - "*porechop.log"
-      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
+      extra: |
+        ℹ️: if you get the error message 'Error - was not able to plot data.'
+        this means that porechop did not detect any adapters and therefore no statistics
+        generated.
   - "porechop":
       name: "Porechop_ABI"
       anchor: "porechop_abi"
@@ -124,7 +130,10 @@ top_modules:
       info: "find and remove adapters from Oxford Nanopore reads."
       path_filters:
         - "*porechop_abi.log"
-      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop_abi did not detect any adapters and therefore no statistics generated."
+      extra: |
+        ℹ️: if you get the error message 'Error - was not able to plot data.'
+        this means that porechop_abi did not detect any adapters and therefore no statistics
+        generated.
   - "bowtie2":
       name: "bowtie2"
   - "samtools":
@@ -138,8 +147,13 @@ top_modules:
       anchor: "bracken"
       target: "Bracken"
       doi: "10.7717/peerj-cs.104"
-      info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
-      extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
+      info: |
+        Estimates species abundances in metagenomics samples by probabilistically
+        re-distributing reads in the taxonomic tree.
+      extra: |
+        ℹ️: plot title will say Kraken2 due to the first step of bracken producing
+        the same output format as Kraken. Abundance information is currently not supported
+        in MultiQC.
       path_filters:
         - "*.bracken.kraken2.report.txt"
   - "kraken":
@@ -147,8 +161,15 @@ top_modules:
       anchor: "centrifuge"
       target: "Centrifuge"
       doi: "10.1101/gr.210641.116"
-      info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title"
-      extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
+      info: |
+        is a very rapid and memory-efficient system for the classification of DNA
+        sequences from microbial samples. The system uses a novel indexing scheme based
+        on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
+        Note: Figure title
+      extra: |
+        ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
+        format as Kraken. If activated, see the actual Kraken2 results in the section
+        above.
       path_filters:
         - "*.centrifuge.txt"
   - "malt":
@@ -266,29 +287,29 @@ table_columns_placement:
 
 table_columns_visible:
   FastQC / Falco (pre-Trimming):
-    total_sequences: True
-    avg_sequence_length: True
-    percent_duplicates: True
-    percent_gc: True
-    percent_fails: False
+    total_sequences: true
+    avg_sequence_length: true
+    percent_duplicates: true
+    percent_gc: true
+    percent_fails: false
   FastQC / Falco (post-Trimming):
-    total_sequences: True
-    avg_sequence_length: True
-    percent_duplicates: False
-    percent_gc: False
-    percent_fails: False
+    total_sequences: true
+    avg_sequence_length: true
+    percent_duplicates: false
+    percent_gc: false
+    percent_fails: false
   Adapter Removal:
-    aligned_total: True
-    percent_aligned: True
-    percent_collapsed: True
-    percent_discarded: False
+    aligned_total: true
+    percent_aligned: true
+    percent_collapsed: true
+    percent_discarded: false
   fastp:
-    pct_adapter: True
-    pct_surviving: True
-    pct_duplication: False
-    after_filtering_gc_content: False
-    after_filtering_q30_rate: False
-    after_filtering_q30_bases: False
+    pct_adapter: true
+    pct_surviving: true
+    pct_duplication: false
+    after_filtering_gc_content: false
+    after_filtering_q30_rate: false
+    after_filtering_q30_bases: false
   nonpareil:
     nonpareil_R: false
     nonpareil_LR: false
@@ -296,51 +317,51 @@ table_columns_visible:
     nonpareil_C: true
     nonpareil_diversity: true
   porechop:
-    Input reads: False
+    Input reads: false
     Start Trimmed:
-    Start Trimmed Percent: True
-    End Trimmed: False
-    End Trimmed Percent: True
-    Middle Split: False
-    Middle Split Percent: True
+    Start Trimmed Percent: true
+    End Trimmed: false
+    End Trimmed Percent: true
+    Middle Split: false
+    Middle Split Percent: true
   porechop_abi:
-    Input reads: False
+    Input reads: false
     Start Trimmed:
-    Start Trimmed Percent: True
-    End Trimmed: False
-    End Trimmed Percent: True
-    Middle Split: False
-    Middle Split Percent: True
+    Start Trimmed Percent: true
+    End Trimmed: false
+    End Trimmed Percent: true
+    Middle Split: false
+    Middle Split Percent: true
   Filtlong:
-    Target bases: True
+    Target bases: true
   nanoq:
-    ReadN50: True
-    Reads: True
+    ReadN50: true
+    Reads: true
   BBDuk:
-    Input reads: False
-    Total Removed bases Percent: False
-    Total Removed bases: False
-    Total Removed reads percent: True
-    Total Removed reads: False
+    Input reads: false
+    Total Removed bases Percent: false
+    Total Removed bases: false
+    Total Removed reads percent: true
+    Total Removed reads: false
   "PRINSEQ++":
-    prinseqplusplus_total: True
+    prinseqplusplus_total: true
   bowtie2:
-    overall_alignment_rate: True
+    overall_alignment_rate: true
   Samtools Stats:
-    raw_total_sequences: True
-    reads_mapped: True
-    reads_mapped_percent: True
-    reads_properly_paired_percent: False
-    non-primary_alignments: False
-    reads_MQ0_percent: False
-    error_rate: False
-  Kraken: False
-  Bracken: False
-  Centrifuge: False
-  DIAMOND: False
-  Kaiju: False
-  MALT: False
-  motus: False
+    raw_total_sequences: true
+    reads_mapped: true
+    reads_mapped_percent: true
+    reads_properly_paired_percent: false
+    non-primary_alignments: false
+    reads_MQ0_percent: false
+    error_rate: false
+  Kraken: false
+  Bracken: false
+  Centrifuge: false
+  DIAMOND: false
+  Kaiju: false
+  MALT: false
+  motus: false
 
 table_columns_name:
   FastQC / Falco (pre-Trimming):
@@ -375,4 +396,5 @@ extra_fn_clean_exts:
     pattern: "_falco"
 
 section_comments:
-  general_stats: "By default, all read count columns are displayed as millions (M) of reads."
+  general_stats: |
+    By default, all read count columns are displayed as millions (M) of reads.
diff --git a/assets/schema_database.json b/assets/schema_database.json
index ec04e326..7706b019 100644
--- a/assets/schema_database.json
+++ b/assets/schema_database.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/taxprofiler/master/assets/schema_database.json",
     "title": "nf-core/taxprofiler pipeline - params.database schema",
     "description": "Schema for the file provided with params.database",
@@ -9,7 +9,6 @@
         "properties": {
             "tool": {
                 "type": "string",
-                "exists": true,
                 "enum": [
                     "bracken",
                     "centrifuge",
@@ -28,7 +27,6 @@
             },
             "db_name": {
                 "type": "string",
-                "exists": true,
                 "pattern": "^\\S+$",
                 "errorMessage": "The unique name of the database should be provided.",
                 "meta": ["db_name"]
@@ -52,7 +50,7 @@
                 "errorMessage": "db_path should be either a file path or a directory."
             }
         },
-        "required": ["tool", "db_name", "db_path"],
-        "uniqueEntries": ["tool", "db_name"]
-    }
+        "required": ["tool", "db_name", "db_path"]
+    },
+    "uniqueEntries": ["tool", "db_name"]
 }
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 0536930b..1d7e9499 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",
     "$id": "https://raw.githubusercontent.com/nf-core/taxprofiler/master/assets/schema_input.json",
     "title": "nf-core/taxprofiler pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -8,13 +8,14 @@
         "type": "object",
         "properties": {
             "sample": {
-                "type": "string",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "type": ["string", "integer"],
+                "pattern": "^[^\\s]+$",
+                "errorMessage": "Sample name must be a string or an integer and cannot contain spaces",
                 "meta": ["id"]
             },
             "run_accession": {
-                "type": "string",
-                "unique": ["sample"],
+                "type": ["string", "integer"],
+                "pattern": "^[^\\s]+$",
                 "errorMessage": "Run accession must be provided and cannot contain spaces."
             },
             "instrument_platform": {
@@ -36,26 +37,32 @@
             },
             "fastq_1": {
                 "type": "string",
+                "exists": true,
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "unique": true,
                 "errorMessage": "Gzipped FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
+                "exists": true,
                 "format": "file-path",
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "unique": true,
                 "errorMessage": "Gzipped FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'. If not applicable, leave it empty."
             },
             "fasta": {
                 "type": "string",
+                "exists": true,
                 "format": "file-path",
                 "pattern": "^\\S+\\.(fasta|fas|fna|fa)\\.gz?$",
-                "unique": true,
                 "errorMessage": "Gzipped FastA file must be provided, cannot contain spaces and must have extension '.fa.gz', 'fna.gz', 'fas.gz', or '.fasta.gz'. If not applicable, leave it empty."
             }
         },
         "required": ["sample", "run_accession", "instrument_platform"]
-    }
+    },
+    "allOf": [
+        { "uniqueEntries": ["fastq_1"] },
+        { "uniqueEntries": ["fastq_2"] },
+        { "uniqueEntries": ["fasta"] },
+        { "uniqueEntries": ["sample", "run_accession"] }
+    ]
 }
diff --git a/conf/base.config b/conf/base.config
index 6a116bf8..595feef9 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,45 +10,45 @@
 
 process {
 
-    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
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 1.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = {  1                   }
+        memory = {  1.GB * task.attempt }
+        time   = {  4.h  * task.attempt }
     }
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { 2     * task.attempt }
+        memory = { 12.GB * task.attempt }
+        time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { 6     * task.attempt }
+        memory = { 36.GB * task.attempt }
+        time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
-        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+        cpus   = { 12    * task.attempt }
+        memory = { 72.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'
@@ -71,18 +71,18 @@ process {
     }
 
     withName: MEGAN_RMA2INFO_TSV {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withName: MEGAN_RMA2INFO_KRONA {
-        cpus   = { check_max( 1                  , 'cpus'    ) }
-        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 1                   }
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
     withName: FALCO {
-        cpus   = { check_max( 6                  , 'cpus'    ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+        cpus   = { 6                   }
+        memory = { 4.GB * task.attempt }
+        time   = { 4.h  * task.attempt }
     }
 }
diff --git a/conf/igenomes.config b/conf/igenomes.config
deleted file mode 100644
index 3f114377..00000000
--- a/conf/igenomes.config
+++ /dev/null
@@ -1,440 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for iGenomes paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines reference genomes using iGenome paths.
-    Can be used by any config that customises the base path using:
-        $params.igenomes_base / --igenomes_base
-----------------------------------------------------------------------------------------
-*/
-
-params {
-    // illumina iGenomes reference file paths
-    genomes {
-        'GRCh37' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
-        }
-        'GRCh38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'CHM13' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
-            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
-            mito_name   = "chrM"
-        }
-        'GRCm38' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
-        }
-        'TAIR10' {
-            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-            mito_name   = "Mt"
-        }
-        'EB2' {
-            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
-        }
-        'UMD3.1' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'WBcel235' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
-            mito_name   = "MtDNA"
-            macs_gsize  = "9e7"
-        }
-        'CanFam3.1' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'GRCz10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'BDGP6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
-            mito_name   = "M"
-            macs_gsize  = "1.2e8"
-        }
-        'EquCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'EB1' {
-            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Gm01' {
-            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'IRGSP-1.0' {
-            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'CHIMP2.1.4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'Rnor_5.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'Rnor_6.0' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-        }
-        'R64-1-1' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
-            mito_name   = "MT"
-            macs_gsize  = "1.2e7"
-        }
-        'EF2' {
-            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-            mito_name   = "MT"
-            macs_gsize  = "1.21e7"
-        }
-        'Sbi1' {
-            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
-        }
-        'Sscrofa10.2' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-            mito_name   = "MT"
-        }
-        'AGPv3' {
-            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
-            mito_name   = "Mt"
-        }
-        'hg38' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
-        }
-        'hg19' {
-            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "2.7e9"
-            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
-        }
-        'mm10' {
-            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.87e9"
-            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
-        }
-        'bosTau8' {
-            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'ce10' {
-            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "9e7"
-        }
-        'canFam3' {
-            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'danRer10' {
-            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.37e9"
-        }
-        'dm6' {
-            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e8"
-        }
-        'equCab2' {
-            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'galGal4' {
-            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'panTro4' {
-            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-        'rn6' {
-            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
-            mito_name   = "chrM"
-        }
-        'sacCer3' {
-            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
-            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-            mito_name   = "chrM"
-            macs_gsize  = "1.2e7"
-        }
-        'susScr3' {
-            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
-            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
-            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
-            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
-            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
-            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
-            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
-            mito_name   = "chrM"
-        }
-    }
-}
diff --git a/conf/test.config b/conf/test.config
index 4e457585..610a1d01 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,15 +10,18 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.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
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -52,16 +55,40 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: MEGAN_RMA2INFO_TSV {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = "-c2c Taxonomy"
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{txt.gz,megan}'
+        ]
     }
     withName: MEGAN_RMA2INFO_KRONA {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "--read2class Taxonomy" }
+        ext.prefix = { "${meta.id}_${meta.db_name}" }
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_alternativepreprocessing.config b/conf/test_alternativepreprocessing.config
index 6c6cb1aa..b67c06e2 100644
--- a/conf/test_alternativepreprocessing.config
+++ b/conf/test_alternativepreprocessing.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                = 'Test profile for adapterremoval'
     config_profile_description         = "Minimal test to check the alternative short-read QC function, adapterremoval"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                           = 2
-    max_memory                         = '6.GB'
-    max_time                           = '6.h'
-
     // Input data
     input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -47,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_bbduk.config b/conf/test_bbduk.config
index 184dabea..3dafb0ff 100644
--- a/conf/test_bbduk.config
+++ b/conf/test_bbduk.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                = 'Test profile for bbduk'
     config_profile_description         = "Minimal test to check the default tool of short-read complexity filtering, bbduk"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                           = 2
-    max_memory                         = '6.GB'
-    max_time                           = '6.h'
-
     // Input data
     input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -45,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_falco.config b/conf/test_falco.config
index 313a6507..17e11f37 100644
--- a/conf/test_falco.config
+++ b/conf/test_falco.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                = 'Test profile for Falco'
     config_profile_description         = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function but running falco instead of fastqc. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                           = 2
-    max_memory                         = '6.GB'
-    max_time                           = '6.h'
-
     // Input data
     input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -45,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_fastp.config b/conf/test_fastp.config
index f68189e9..b59af972 100644
--- a/conf/test_fastp.config
+++ b/conf/test_fastp.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile for fastp'
     config_profile_description             = "Minimal test to check the default short-read QC function, fastp"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                               = 2
-    max_memory                             = '6.GB'
-    max_time                               = '6.h'
-
     // Input data
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -47,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_krakenuniq.config b/conf/test_krakenuniq.config
index de3c50da..3fb2791d 100644
--- a/conf/test_krakenuniq.config
+++ b/conf/test_krakenuniq.config
@@ -14,15 +14,19 @@
 // Separate test as KrakenUniq database can sometimes be too big for GHA
 //
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test to check KrakenUniq function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input                                   = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                               = params.pipelines_testdata_base_path + 'taxprofiler/database_krakenuniq.csv'
@@ -57,15 +61,40 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: MEGAN_RMA2INFO_TSV {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = "-c2c Taxonomy"
+        ext.prefix = { "${meta.id}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{txt.gz,megan}'
+        ]
     }
     withName: MEGAN_RMA2INFO_KRONA {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "--read2class Taxonomy" }
+        ext.prefix = { "${meta.id}_${meta.db_name}" }
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_malt.config b/conf/test_malt.config
index 701453c6..9e144d3d 100644
--- a/conf/test_malt.config
+++ b/conf/test_malt.config
@@ -14,15 +14,19 @@
 // Separate test for malt
 //
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile'
     config_profile_description             = 'Minimal test to check malt function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                               = 2
-    max_memory                             = '6.GB'
-    max_time                               = '6.h'
-
     // Input data
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_malt.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -49,9 +53,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_motus.config b/conf/test_motus.config
index 1152d2ae..fe9d3e0a 100644
--- a/conf/test_motus.config
+++ b/conf/test_motus.config
@@ -14,15 +14,19 @@
 // Separate test as mOTUs database download can be flaky
 //
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name        = 'mOTUs Test profile'
     config_profile_description = 'Minimal test to check mOTUs function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input                                   = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                               = 'database_motus.csv'
@@ -53,9 +57,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config
index 23ab7214..c31281d8 100644
--- a/conf/test_nopreprocessing.config
+++ b/conf/test_nopreprocessing.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile'
     config_profile_description             = 'Minimal test dataset skipping all preprocessing 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
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -47,10 +51,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config
index 70e238ee..ea91f489 100644
--- a/conf/test_noprofiling.config
+++ b/conf/test_noprofiling.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile'
     config_profile_description             = 'Minimal test dataset without performing any profiling 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
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -46,9 +50,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index e8b87bc7..5d22558a 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile'
     config_profile_description             = "Minimal test dataset without performing any preprocessing nor profiling to check pipeline function. Useful when you only wish to test a single profiler without having to 'opt-out' of all the others"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                               = 2
-    max_memory                             = '6.GB'
-    max_time                               = '6.h'
-
     // Input data
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -45,10 +49,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/conf/test_prinseqplusplus.config b/conf/test_prinseqplusplus.config
index d9c576f4..6abb95fa 100644
--- a/conf/test_prinseqplusplus.config
+++ b/conf/test_prinseqplusplus.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    // Limit resources so that this can run on GitHub Actions
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '6.h'
+    ]
+}
+
 params {
     config_profile_name                    = 'Test profile for prinseqplusplus'
     config_profile_description             = "Minimal test to check the alternative tool of short-read complexity filtering, prinseqplusplus"
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus                               = 2
-    max_memory                             = '6.GB'
-    max_time                               = '6.h'
-
     // Input data
     input                                  = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
     databases                              = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.2.csv'
@@ -46,10 +50,23 @@ params {
 
 process {
     withName: MALT_RUN {
+        tag = {"${meta.db_name}|${meta.id}"}
         maxForks = 1
-        ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
+        ext.args = { "${meta.db_params} -m ${params.malt_mode} -J-Xmx12G" }
+        ext.prefix = { "${meta.db_name}" }
+        publishDir = [
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{rma6,log,sam}'
+        ]
     }
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/nonpareil/" },
+            mode: params.publish_dir_mode,
+            pattern: '*.np{a,c,l,o}'
+        ]
     }
 }
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
index 361d0e47..00000000
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 cb39ebb8..00000000
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 a4b89bf5..00000000
Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ
diff --git a/docs/images/taxprofiler_tube_darkmode.pdf b/docs/images/taxprofiler_tube_darkmode.pdf
new file mode 100644
index 00000000..ee5f85e7
Binary files /dev/null and b/docs/images/taxprofiler_tube_darkmode.pdf differ
diff --git a/docs/images/taxprofiler_tube_darkmode.png b/docs/images/taxprofiler_tube_darkmode.png
new file mode 100644
index 00000000..9adb5d48
Binary files /dev/null and b/docs/images/taxprofiler_tube_darkmode.png differ
diff --git a/docs/images/taxprofiler_tube_darkmode.svg b/docs/images/taxprofiler_tube_darkmode.svg
new file mode 100644
index 00000000..d52b1677
--- /dev/null
+++ b/docs/images/taxprofiler_tube_darkmode.svg
@@ -0,0 +1,5344 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="2161.4099"
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+   id="svg5"
+   inkscape:version="1.3.2 (1:1.3.2+202311252150+091e20ef0f)"
+   sodipodi:docname="taxprofiler_tube_darkmode.svg"
+   xml:space="preserve"
+   inkscape:export-filename="taxprofiler_tube_darkmode.png"
+   inkscape:export-xdpi="300"
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diff --git a/docs/usage.md b/docs/usage.md
index d9e44bc1..30894274 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -225,9 +225,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -235,12 +234,11 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run nf-core/taxprofiler -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
-```yaml
+```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
 <...>
 ```
 
@@ -470,23 +468,21 @@ nextflow pull nf-core/taxprofiler
 
 ### Reproducibility
 
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/taxprofiler releases page](https://github.com/nf-core/taxprofiler/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
 
 ### `-profile`
 
@@ -494,11 +490,10 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
@@ -539,13 +534,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 ### Resource requests
 
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
@@ -563,14 +558,6 @@ 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/docs/usage/tutorials.md b/docs/usage/tutorials.md
index aa48a200..251f1aca 100644
--- a/docs/usage/tutorials.md
+++ b/docs/usage/tutorials.md
@@ -123,8 +123,7 @@ nextflow run nf-core/taxprofiler -r 1.1.0 -profile docker \
 --perform_shortread_hostremoval --hostremoval_reference GCF_000819615.1_ViralProj14015_genomic.fna.gz \
 --perform_runmerging --save_runmerged_reads \
 --run_centrifuge --run_kaiju --run_kraken2 \
---run_profile_standardisation \
---max_cpus 2 --max_memory '6.GB'
+--run_profile_standardisation
 ```
 
 :::info
@@ -144,9 +143,7 @@ To break down each line of the command:
 - (Optional) provide a _cap_ to the maximum amount of resources each step/job of the pipeline can use
 
 :::warning
-The `--max_cpu`, `--max_memory`, `--max_time` parameters _do not_ increase the amount of memory a step of the pipeline uses!
-They simply prevent Nextflow requesting more than this threshold, e.g. more than available on your machine.
-To learn how to increase computational resource to the pipeline, see the central [nf-core documentation](https://nf-co.re/docs/usage/configuration).
+The pipeline runs occasionally fail due to a particular step of the pipeline requesting more resources than you have on your system. To avoid these failures, you can tell Nextflow to set a cap pipeline-step resource requests against a list called `resourceLimits` specified in Nextflow config file. These should represent the maximum possible resources of a machine or node. To learn how to increase computational resource to the pipeline, see the central [nf-core documentation](https://nf-co.re/docs/usage/configuration).
 :::
 
 The pipeline run can be represented (in a simplified format!) as follows
diff --git a/main.nf b/main.nf
index 1cca7494..afb15c49 100644
--- a/main.nf
+++ b/main.nf
@@ -9,8 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
@@ -27,8 +25,6 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_taxp
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -53,10 +49,8 @@ workflow NFCORE_TAXPROFILER {
         samplesheet,
         databases,
     )
-
     emit:
     multiqc_report = TAXPROFILER.out.multiqc_report // channel: /path/to/multiqc_report.html
-
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -67,13 +61,11 @@ workflow NFCORE_TAXPROFILER {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
         params.validate_params,
         params.monochrome_logs,
         args,
@@ -89,7 +81,6 @@ workflow {
         PIPELINE_INITIALISATION.out.samplesheet,
         PIPELINE_INITIALISATION.out.databases,
     )
-
     //
     // SUBWORKFLOW: Run completion tasks
     //
diff --git a/modules.json b/modules.json
index 77bf8131..e8fa606a 100644
--- a/modules.json
+++ b/modules.json
@@ -42,12 +42,12 @@
                     },
                     "centrifuge/centrifuge": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "8581a564b0acbe28e222570ce395278f91705dc5",
                         "installed_by": ["modules"]
                     },
                     "centrifuge/kreport": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "8581a564b0acbe28e222570ce395278f91705dc5",
                         "installed_by": ["modules"]
                     },
                     "diamond/blastx": {
@@ -67,7 +67,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "filtlong": {
@@ -137,7 +137,7 @@
                     },
                     "krakenuniq/preloadedkrakenuniq": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "2512434a59d282cba0fbc53ddb81dd8f244dc428",
                         "installed_by": ["modules"]
                     },
                     "krona/ktimporttaxonomy": {
@@ -192,7 +192,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653",
+                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
                         "installed_by": ["modules"]
                     },
                     "nanoq": {
@@ -202,7 +202,7 @@
                     },
                     "nonpareil/curve": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "63a1d0afbf5f129fb00a2acea5aa627915b288cd",
                         "installed_by": ["modules"]
                     },
                     "nonpareil/nonpareil": {
@@ -277,17 +277,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml
index 42592891..b49177e9 100644
--- a/modules/nf-core/centrifuge/centrifuge/environment.yml
+++ b/modules/nf-core/centrifuge/centrifuge/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/centrifuge/main.nf b/modules/nf-core/centrifuge/centrifuge/main.nf
index d9a5653d..f287dc25 100644
--- a/modules/nf-core/centrifuge/centrifuge/main.nf
+++ b/modules/nf-core/centrifuge/centrifuge/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_CENTRIFUGE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(reads)
@@ -14,12 +14,12 @@ process CENTRIFUGE_CENTRIFUGE {
     val save_aligned
 
     output:
-    tuple val(meta), path('*report.txt')                 , emit: report
-    tuple val(meta), path('*results.txt')                , emit: results
-    tuple val(meta), path('*.{sam,tab}')                 , optional: true, emit: sam
-    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')   , optional: true, emit: fastq_mapped
-    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
-    path "versions.yml"                                  , emit: versions
+    tuple val(meta), path('*report.txt'), emit: report
+    tuple val(meta), path('*results.txt'), emit: results
+    tuple val(meta), path('*.{sam,tab}'), optional: true, emit: sam
+    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_mapped
+    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz'), optional: true, emit: fastq_unmapped
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,13 +27,14 @@ process CENTRIFUGE_CENTRIFUGE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
@@ -49,13 +50,13 @@ process CENTRIFUGE_CENTRIFUGE {
     centrifuge \\
         -x \$db_name \\
         --temp-directory ./temp \\
-        -p $task.cpus \\
-        $paired \\
+        -p ${task.cpus} \\
+        ${paired} \\
         --report-file ${prefix}.report.txt \\
         -S ${prefix}.results.txt \\
-        $unaligned \\
-        $aligned \\
-        $args
+        ${unaligned} \\
+        ${aligned} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -64,15 +65,16 @@ process CENTRIFUGE_CENTRIFUGE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def _paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
     def unaligned = ''
     def aligned = ''
     if (meta.single_end) {
         unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
-    } else {
+    }
+    else {
         unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         aligned = save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
     }
diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml
index a06104e1..17329e93 100644
--- a/modules/nf-core/centrifuge/centrifuge/meta.yml
+++ b/modules/nf-core/centrifuge/centrifuge/meta.yml
@@ -12,59 +12,86 @@ tools:
       documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
       doi: 10.1101/gr.210641.116
       licence: ["GPL v3"]
+      identifier: biotools:centrifuge
 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.
-  - db:
-      type: directory
-      description: Path to directory containing centrifuge database files
-  - save_unaligned:
-      type: boolean
-      description: If true unmapped fastq files are saved
-  - save_aligned:
-      type: boolean
-      description: If true mapped fastq files are saved
+  - - 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.
+  - - db:
+        type: directory
+        description: Path to directory containing centrifuge database files
+  - - save_unaligned:
+        type: boolean
+        description: If true unmapped fastq files are saved
+  - - save_aligned:
+        type: boolean
+        description: If true mapped fastq files are saved
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - report:
-      type: file
-      description: |
-        File containing a classification summary
-      pattern: "*.{report.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*report.txt":
+          type: file
+          description: |
+            File containing a classification summary
+          pattern: "*.{report.txt}"
   - results:
-      type: file
-      description: |
-        File containing classification results
-      pattern: "*.{results.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*results.txt":
+          type: file
+          description: |
+            File containing classification results
+          pattern: "*.{results.txt}"
   - sam:
-      type: file
-      description: |
-        Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
-      pattern: "*.{sam,tab}"
-  - fastq_unmapped:
-      type: file
-      description: Unmapped fastq files
-      pattern: "*.unmapped.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{sam,tab}":
+          type: file
+          description: |
+            Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s
+          pattern: "*.{sam,tab}"
   - fastq_mapped:
-      type: file
-      description: Mapped fastq files
-      pattern: "*.mapped.fastq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.mapped.fastq{,.1,.2}.gz":
+          type: file
+          description: Mapped fastq files
+          pattern: "*.mapped.fastq.gz"
+  - fastq_unmapped:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.unmapped.fastq{,.1,.2}.gz":
+          type: file
+          description: Unmapped fastq files
+          pattern: "*.unmapped.fastq.gz"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@sofstam"
   - "@jfy133"
diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml
index 42592891..b49177e9 100644
--- a/modules/nf-core/centrifuge/kreport/environment.yml
+++ b/modules/nf-core/centrifuge/kreport/environment.yml
@@ -1,5 +1,6 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - bioconda::centrifuge=1.0.4.1
+  - bioconda::centrifuge=1.0.4.2
diff --git a/modules/nf-core/centrifuge/kreport/main.nf b/modules/nf-core/centrifuge/kreport/main.nf
index 25eb7167..b7e83604 100644
--- a/modules/nf-core/centrifuge/kreport/main.nf
+++ b/modules/nf-core/centrifuge/kreport/main.nf
@@ -1,11 +1,11 @@
 process CENTRIFUGE_KREPORT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.1--hdcf5f25_1' :
-        'biocontainers/centrifuge:1.0.4.1--hdcf5f25_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4.2--hdcf5f25_0'
+        : 'biocontainers/centrifuge:1.0.4.2--hdcf5f25_0'}"
 
     input:
     tuple val(meta), path(report)
@@ -13,7 +13,7 @@ process CENTRIFUGE_KREPORT {
 
     output:
     tuple val(meta), path('*.txt'), emit: kreport
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,7 +23,10 @@ process CENTRIFUGE_KREPORT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     db_name=`find -L ${db} -name "*.1.cf" -not -name "._*"  | sed 's/\\.1.cf\$//'`
-    centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
+    centrifuge-kreport \\
+        ${args} \\
+        -x \$db_name \\
+        ${report} > ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -32,7 +35,7 @@ process CENTRIFUGE_KREPORT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def _args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt
diff --git a/modules/nf-core/centrifuge/kreport/meta.yml b/modules/nf-core/centrifuge/kreport/meta.yml
index 5641152b..e195eebf 100644
--- a/modules/nf-core/centrifuge/kreport/meta.yml
+++ b/modules/nf-core/centrifuge/kreport/meta.yml
@@ -14,35 +14,38 @@ tools:
       documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml
       doi: 10.1101/gr.210641.116
       licence: ["GPL v3"]
+      identifier: biotools:centrifuge
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - report:
-      type: file
-      description: File containing the centrifuge classification report
-      pattern: "*.{txt}"
-  - db:
-      type: directory
-      description: Path to directory containing centrifuge database files
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - report:
+        type: file
+        description: File containing the centrifuge classification report
+        pattern: "*.{txt}"
+  - - db:
+        type: directory
+        description: Path to directory containing centrifuge database files
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - kreport:
-      type: file
-      description: |
-        File containing kraken-style report from centrifuge
-        out files.
-      pattern: "*.{txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.txt":
+          type: file
+          description: |
+            File containing kraken-style report from centrifuge
+            out files.
+          pattern: "*.{txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@sofstam"
   - "@jfy133"
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d8989f48..033f4154 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -1,5 +1,5 @@
 process FASTQC {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -19,30 +19,30 @@ process FASTQC {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args          = task.ext.args ?: ''
+    def prefix        = task.ext.prefix ?: "${meta.id}"
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    def rename_to     = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // 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
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
     """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        --memory $fastqc_memory \\
-        $renamed_files
+        ${args} \\
+        --threads ${task.cpus} \\
+        --memory ${fastqc_memory} \\
+        ${renamed_files}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e0..2b2e62b8 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,40 +11,50 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       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/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
deleted file mode 100644
index 7834294b..00000000
--- a/modules/nf-core/fastqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqc:
-  - modules/nf-core/fastqc/**
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
index d24f75d2..3a31fcb4 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/main.nf
@@ -8,7 +8,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }"
 
     input:
-    tuple val(meta), path(sequences)
+    // We stage sequencing files in a sub-directory so we don't accidentally gzip them later.
+    tuple val(meta), path(sequences, name: 'sequences/*'), val(prefixes)
     val sequence_type
     path db
     val ram_chunk_size
@@ -28,6 +29,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
 
     script:
     assert sequence_type in ['fasta', 'fastq']
+    sequences = sequences instanceof List ? sequences : [sequences]
 
     def args = task.ext.args ?: ''
     def args2 = task.ext.args ?: ''
@@ -38,9 +40,20 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     unclassified_option = save_output_reads ? "--unclassified-out \"${unclassified}\"" : ''
     def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
     def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
-    compress_reads_command = save_output_reads ? "find . -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
+    compress_reads_command = save_output_reads ? "find . -maxdepth 0 -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
+    def command_inputs_file = '.inputs.txt'
+
     if (meta.single_end) {
+        assert sequences.size() == prefixes.size()
+        command_inputs = [sequences, prefixes].transpose().collect { seq, prefix -> "${seq}\t${prefix}" }
+
         """
+        # Store the batch of samples for later command input.
+        cat <<-END_INPUTS > ${command_inputs_file}
+        ${command_inputs.join('\n        ')}
+        END_INPUTS
+
+        # Preload the KrakenUniq database into memory.
         krakenuniq \\
             $args \\
             --db $db \\
@@ -48,15 +61,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             --preload-size $ram_chunk_size \\
             --threads $task.cpus
 
-        strip_suffix() {
-            local result=\$1
-            # Strip any file extensions.
-            echo "\${result%%.*}"
-        }
-
-        printf "%s\\n" ${sequences} | while read FASTQ; do \\
-            PREFIX="\$(strip_suffix "\${FASTQ}")"
-
+        # Run the KrakenUniq classification on each sample in the batch.
+        while IFS='\t' read -r SEQ PREFIX; do
             krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
@@ -65,8 +71,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $unclassified_option \\
                 $classified_option \\
                 $args2 \\
-                "\${FASTQ}"
-        done
+                "\${SEQ}"
+        done < ${command_inputs_file}
 
         $compress_reads_command
 
@@ -76,7 +82,16 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         END_VERSIONS
         """
     } else {
+        assert sequences.size() / 2 == prefixes.size()
+        command_inputs = [sequences.collate(2), prefixes].transpose().collect { pair, prefix -> "${pair[0]}\t${pair[1]}\t${prefix}" }
+
         """
+        # Store the batch of samples for later command input.
+        cat <<-END_INPUTS > ${command_inputs_file}
+        ${command_inputs.join('\n        ')}
+        END_INPUTS
+
+        # Preload the KrakenUniq database into memory.
         krakenuniq \\
             $args \\
             --db $db \\
@@ -84,18 +99,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             --preload-size $ram_chunk_size \\
             --threads $task.cpus
 
-        strip_suffix() {
-            local result
-            read result
-            # Strip any trailing dot or underscore.
-            result="\${result%_}"
-            echo "\${result%.}"
-        }
-
-        printf "%s %s\\n" ${sequences} | while read FASTQ; do \\
-            read -r -a FASTQ <<< "\${FASTQ}"
-            PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
-
+        # Run the KrakenUniq classification on each sample in the batch.
+        while IFS='\t' read -r FIRST_SEQ SECOND_SEQ PREFIX; do
             krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
@@ -105,8 +110,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $classified_option \\
                 --paired \\
                 $args2 \\
-                "\${FASTQ[@]}"
-        done
+                "\${FIRST_SEQ}" "\${SECOND_SEQ}"
+        done < ${command_inputs_file}
 
         $compress_reads_command
 
@@ -119,6 +124,7 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
 
     stub:
     assert sequence_type in ['fasta', 'fastq']
+    sequences = sequences instanceof List ? sequences : [sequences]
 
     def args = task.ext.args ?: ''
     def args2 = task.ext.args ?: ''
@@ -130,8 +136,19 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
     def output_option = save_output ? '--output "\${PREFIX}.krakenuniq.classified.txt"' : ''
     def report = report_file ? '--report-file "\${PREFIX}.krakenuniq.report.txt"' : ''
     compress_reads_command = save_output_reads ? "find . -name '*.${sequence_type}' -print0 | xargs -0 -t -P ${task.cpus} -I % gzip --no-name %" : ''
+    def command_inputs_file = '.inputs.txt'
+
     if (meta.single_end) {
+        assert sequences.size() == prefixes.size()
+        command_inputs = [sequences, prefixes].transpose().collect { seq, prefix -> "${seq}\t${prefix}" }
+
         """
+        # Store the batch of samples for later command input.
+        cat <<-END_INPUTS > ${command_inputs_file}
+        ${command_inputs.join('\n        ')}
+        END_INPUTS
+
+        # Preload the KrakenUniq database into memory.
         echo krakenuniq \\
             $args \\
             --db $db \\
@@ -139,12 +156,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             --preload-size $ram_chunk_size \\
             --threads $task.cpus
 
-        strip_suffix() {
-            local result=\$1
-            # Strip any file extensions.
-            echo "\${result%%.*}"
-        }
-
         create_file() {
             echo '<3 nf-core' > "\$1"
         }
@@ -153,11 +164,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             echo '<3 nf-core' | gzip -n > "\$1"
         }
 
-        printf "%s\\n" ${sequences} | while read FASTQ; do \\
-            echo "\${FASTQ}"
-            PREFIX="\$(strip_suffix "\${FASTQ}")"
-            echo "\${PREFIX}"
-
+        # Run the KrakenUniq classification on each sample in the batch.
+        while IFS='\t' read -r SEQ PREFIX; do
             echo krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
@@ -166,13 +174,13 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $unclassified_option \\
                 $classified_option \\
                 $args2 \\
-                "\${FASTQ}"
+                "\${SEQ}"
 
             create_file "\${PREFIX}.krakenuniq.classified.txt"
             create_file "\${PREFIX}.krakenuniq.report.txt"
             create_gzip_file "\${PREFIX}.classified.${sequence_type}.gz"
             create_gzip_file "\${PREFIX}.unclassified.${sequence_type}.gz"
-        done
+        done < ${command_inputs_file}
 
         echo "$compress_reads_command"
 
@@ -182,7 +190,16 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         END_VERSIONS
         """
     } else {
+        assert sequences.size() / 2 == prefixes.size()
+        command_inputs = [sequences.collate(2), prefixes].transpose().collect { pair, prefix -> "${pair[0]}\t${pair[1]}\t${prefix}" }
+
         """
+        # Store the batch of samples for later command input.
+        cat <<-END_INPUTS > ${command_inputs_file}
+        ${command_inputs.join('\n        ')}
+        END_INPUTS
+
+        # Preload the KrakenUniq database into memory.
         echo krakenuniq \\
             $args \\
             --db $db \\
@@ -190,14 +207,6 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             --preload-size $ram_chunk_size \\
             --threads $task.cpus
 
-        strip_suffix() {
-            local result
-            read result
-            # Strip any trailing dot or underscore.
-            result="\${result%_}"
-            echo "\${result%.}"
-        }
-
         create_file() {
             echo '<3 nf-core' > "\$1"
         }
@@ -206,12 +215,8 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
             echo '<3 nf-core' | gzip -n > "\$1"
         }
 
-        printf "%s %s\\n" ${sequences} | while read FASTQ; do \\
-            read -r -a FASTQ <<< "\${FASTQ}"
-            echo "\${FASTQ[@]}"
-            PREFIX="\$(printf "%s\\n" "\${FASTQ[@]}" |  sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' | strip_suffix)"
-            echo "\${PREFIX}"
-
+        # Run the KrakenUniq classification on each sample in the batch.
+        while IFS='\t' read -r FIRST_SEQ SECOND_SEQ PREFIX; do
             echo krakenuniq \\
                 --db $db \\
                 --threads $task.cpus \\
@@ -221,13 +226,13 @@ process KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
                 $classified_option \\
                 --paired \\
                 $args2 \\
-                "\${FASTQ[@]}"
+                "\${FIRST_SEQ}" "\${SECOND_SEQ}"
 
             create_file "\${PREFIX}.krakenuniq.classified.txt"
             create_file "\${PREFIX}.krakenuniq.report.txt"
             create_gzip_file "\${PREFIX}.merged.classified.${sequence_type}.gz"
             create_gzip_file "\${PREFIX}.merged.unclassified.${sequence_type}.gz"
-        done
+        done < ${command_inputs_file}
 
         echo "$compress_reads_command"
 
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
index bb6409a6..8e674504 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml
@@ -8,77 +8,108 @@ keywords:
   - db
 tools:
   - "krakenuniq":
-      description: "Metagenomics classifier with unique k-mer counting for more specific results"
+      description: "Metagenomics classifier with unique k-mer counting for more specific
+        results"
       homepage: https://github.com/fbreitwieser/krakenuniq
       documentation: https://github.com/fbreitwieser/krakenuniq
       doi: 10.1186/s13059-018-1568-0
       licence: ["MIT"]
+      identifier: biotools:KrakenUniq
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - sequences:
-      type: file
-      description: List of input files containing sequences. All of them must be either in FASTA or FASTQ format.
-  - sequence_type:
-      type: string
-      description: Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.
-      pattern: "{fasta,fastq}"
-  - db:
-      type: directory
-      description: KrakenUniq database
-  - ram_chunk_size:
-      type: string
-      description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
-      pattern: "*GB"
-  - save_output_reads:
-      type: boolean
-      description: |
-        Optionally, commands are added to save classified and unclassified reads
-        as FASTQ or FASTA files depending on the input format.  When the input
-        is paired-end, the single output FASTQ contains merged reads.
-  - report_file:
-      type: boolean
-      description: Whether to generate a report of relative abundances.
-  - save_output:
-      type: boolean
-      description: Whether to save a file reporting the taxonomic classification of each input read.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - sequences:
+        type: file
+        description: List of input files containing sequences. All of them must be either
+          in FASTA or FASTQ format.
+    - prefixes:
+        type: string
+        description: >
+          List of sample identifiers or filename prefixes. Must correspond in order and
+          length to the 'sequences', or to the number of sequencing pairs.
+  - - sequence_type:
+        type: string
+        description: Format of all given sequencing files as literal string, either
+          'fasta' or 'fastq'.
+        pattern: "{fasta,fastq}"
+  - - db:
+        type: directory
+        description: KrakenUniq database
+  - - ram_chunk_size:
+        type: string
+        description: Amount of maximum amount of RAM each chunk of database that should
+          be loaded at any one time
+        pattern: "*GB"
+  - - save_output_reads:
+        type: boolean
+        description: |
+          Optionally, commands are added to save classified and unclassified reads
+          as FASTQ or FASTA files depending on the input format.  When the input
+          is paired-end, the single output FASTQ contains merged reads.
+  - - report_file:
+        type: boolean
+        description: Whether to generate a report of relative abundances.
+  - - save_output:
+        type: boolean
+        description: Whether to save a file reporting the taxonomic classification of
+          each input read.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - classified_reads:
-      type: file
-      description: |
-        Reads classified as belonging to any of the taxa
-        in the KrakenUniq reference database.
-      pattern: "*.classified.{fastq,fasta}.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.classified.${sequence_type}.gz":
+          type: file
+          description: |
+            Reads classified as belonging to any of the taxa
+            in the KrakenUniq reference database.
+          pattern: "*.classified.{fastq,fasta}.gz"
   - unclassified_reads:
-      type: file
-      description: |
-        Reads not classified to any of the taxa
-        in the KrakenUniq reference database.
-      pattern: "*.unclassified.{fastq,fasta}.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.unclassified.${sequence_type}.gz":
+          type: file
+          description: |
+            Reads not classified to any of the taxa
+            in the KrakenUniq reference database.
+          pattern: "*.unclassified.{fastq,fasta}.gz"
   - classified_assignment:
-      type: file
-      description: |
-        KrakenUniq output file indicating the taxonomic assignment of
-        each input read ## DOUBLE CHECK!!
-      pattern: "*.krakenuniq.classified.txt"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.krakenuniq.classified.txt":
+          type: file
+          description: |
+            KrakenUniq output file indicating the taxonomic assignment of
+            each input read ## DOUBLE CHECK!!
+          pattern: "*.krakenuniq.classified.txt"
   - report:
-      type: file
-      description: |
-        KrakenUniq report containing statistics about classified
-        and unclassified reads.
-      pattern: "*.krakenuniq.report.txt"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.krakenuniq.report.txt":
+          type: file
+          description: |
+            KrakenUniq report containing statistics about classified
+            and unclassified reads.
+          pattern: "*.krakenuniq.report.txt"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@mjamy"
   - "@Midnighter"
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test
index 9e1d6700..16da8e45 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test
@@ -32,7 +32,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test', single_end:true],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fasta'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -45,13 +49,16 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'genome.krakenuniq.report.txt' },
-                { assert file(process.out.unclassified_reads.get(0).get(1)).name == 'genome.unclassified.fasta.gz' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
+                    process.out.unclassified_reads,
                     process.out.classified_assignment,
                     process.out.versions
                 ).match('fasta') },
@@ -69,7 +76,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test', single_end:true],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fastq'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -82,10 +93,13 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'test_interleaved.krakenuniq.report.txt' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
                     process.out.unclassified_reads,
@@ -108,8 +122,11 @@ nextflow_process {
                     [id:'test', single_end:false],
                     [
                         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/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),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fastq'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -122,13 +139,16 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'test.krakenuniq.report.txt' },
-                { assert file(process.out.unclassified_reads.get(0).get(1)).name == 'test.merged.unclassified.fastq.gz' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
+                    process.out.unclassified_reads,
                     process.out.classified_assignment,
                     process.out.versions
                 ).match('fastq-paired') },
@@ -148,7 +168,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test', single_end:true],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fasta'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -161,11 +185,13 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'genome.krakenuniq.report.txt' },
-                { assert file(process.out.unclassified_reads.get(0).get(1)).name == 'genome.unclassified.fasta.gz' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
                     process.out.unclassified_reads,
@@ -188,7 +214,11 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test', single_end:true],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fastq'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -201,10 +231,13 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'test_interleaved.krakenuniq.report.txt' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
                     process.out.unclassified_reads,
@@ -229,8 +262,11 @@ nextflow_process {
                     [id:'test', single_end:false],
                     [
                         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/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),
+                    ],
+                    ['sample_1', 'sample.2']
                 ]
                 input[1] = 'fastq'
                 input[2] = UNTAR.out.untar.map { it[1] }
@@ -243,10 +279,13 @@ nextflow_process {
         }
 
         then {
+            def reports = process.out.report.get(0).get(1).collect { report -> file(report).name }
+            def expected = ['sample_1.krakenuniq.report.txt', 'sample.2.krakenuniq.report.txt']
+
             assertAll (
                 { assert process.success },
                 // Report contains a timestamp.
-                { assert file(process.out.report.get(0).get(1)).name == 'test.krakenuniq.report.txt' },
+                { assertContainsInAnyOrder(reports, expected) },
                 { assert snapshot(
                     process.out.classified_reads,
                     process.out.unclassified_reads,
diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap
index 2a431be8..ca29cf7d 100644
--- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap
+++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/tests/main.nf.test.snap
@@ -7,7 +7,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test_interleaved.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -16,7 +19,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test_interleaved.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -25,7 +31,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test_interleaved.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -33,30 +42,18 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-06T11:21:36.338887437"
+        "timestamp": "2024-10-30T14:25:43.618168582"
     },
     "fastq-single": {
         "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test_interleaved.classified.fastq.gz:md5,3bd95021a8fbced1be8039b990b28176"
-                ]
+                
             ],
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "test_interleaved.unclassified.fastq.gz:md5,143c7eb70ca93cc2d5ea98767c370424"
-                ]
+                
             ],
             [
                 [
@@ -64,7 +61,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test_interleaved.krakenuniq.classified.txt:md5,88a734a9a9216cb0770a77f36c9f4e78"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,f885fa1cdbfc5460af0772219991bf6d",
+                        "sample_1.krakenuniq.classified.txt:md5,88a734a9a9216cb0770a77f36c9f4e78"
+                    ]
                 ]
             ],
             [
@@ -72,21 +72,18 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-06T11:17:43.586414914"
+        "timestamp": "2024-10-30T15:21:33.941412985"
     },
     "fastq-paired": {
         "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.merged.classified.fastq.gz:md5,dd7651837cce63e6108e28f4f019aedb"
-                ]
+                
+            ],
+            [
+                
             ],
             [
                 [
@@ -94,7 +91,10 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.krakenuniq.classified.txt:md5,ed5e19c7a88312cc04e483ac5f2579cd"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,ed5e19c7a88312cc04e483ac5f2579cd",
+                        "sample_1.krakenuniq.classified.txt:md5,ed5e19c7a88312cc04e483ac5f2579cd"
+                    ]
                 ]
             ],
             [
@@ -102,10 +102,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-06T11:37:46.718293365"
+        "timestamp": "2024-10-30T15:21:43.622100223"
     },
     "fasta-stub": {
         "content": [
@@ -115,7 +115,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "genome.classified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.classified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.classified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -124,7 +127,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "genome.unclassified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.unclassified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.unclassified.fasta.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -133,7 +139,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "genome.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -141,10 +150,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-06T11:28:27.729550991"
+        "timestamp": "2024-10-30T14:25:33.871634213"
     },
     "fastq-paired-stub": {
         "content": [
@@ -154,7 +163,10 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.merged.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.merged.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.merged.classified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -163,7 +175,10 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.merged.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.merged.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.merged.unclassified.fastq.gz:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -172,7 +187,10 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975",
+                        "sample_1.krakenuniq.classified.txt:md5,a5704c35e6b573a45e3a344768fe6975"
+                    ]
                 ]
             ],
             [
@@ -180,21 +198,18 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-05T20:06:20.262529457"
+        "timestamp": "2024-10-30T14:25:54.663232573"
     },
     "fasta": {
         "content": [
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": true
-                    },
-                    "genome.classified.fasta.gz:md5,e73599798195a519ba2565c3f0275b93"
-                ]
+                
+            ],
+            [
+                
             ],
             [
                 [
@@ -202,7 +217,10 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "genome.krakenuniq.classified.txt:md5,8aafacd89a6aac98aaf512df0a7493d1"
+                    [
+                        "sample.2.krakenuniq.classified.txt:md5,8aafacd89a6aac98aaf512df0a7493d1",
+                        "sample_1.krakenuniq.classified.txt:md5,2bea6c2195c400a909a2d4cca2e3045e"
+                    ]
                 ]
             ],
             [
@@ -210,9 +228,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-06T11:36:00.24752418"
+        "timestamp": "2024-10-30T14:45:02.199077563"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 0fe12644..a27122ce 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.25
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index b9ccebdb..58d9313c 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -52,7 +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 382c08cb..b16c1879 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
@@ -12,53 +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}"
-  - 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}"
+  - - 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.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index b779e469..7b7c1322 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:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2025-01-27T09:29:57.631982377"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2025-01-27T09:30:34.743726958"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2025-01-27T09:30:21.44383553"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/nonpareil/curve/main.nf b/modules/nf-core/nonpareil/curve/main.nf
index dbe56b26..99651f37 100644
--- a/modules/nf-core/nonpareil/curve/main.nf
+++ b/modules/nf-core/nonpareil/curve/main.nf
@@ -11,7 +11,7 @@ process NONPAREIL_CURVE {
     tuple val(meta), path(npo)
 
     output:
-    tuple val(meta), path("*.png"), emit: png
+    tuple val(meta), path("*.png"), optional: true, emit: png
     path "versions.yml"           , emit: versions
 
     when:
diff --git a/modules/nf-core/nonpareil/curve/meta.yml b/modules/nf-core/nonpareil/curve/meta.yml
index 87aaa363..cd80f16f 100644
--- a/modules/nf-core/nonpareil/curve/meta.yml
+++ b/modules/nf-core/nonpareil/curve/meta.yml
@@ -1,7 +1,7 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "nonpareil_curve"
-description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file
+description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil
+  npo file
 keywords:
   - metagenomics
   - statistics
@@ -18,30 +18,33 @@ tools:
       tool_dev_url: "https://github.com/lmrodriguezr/nonpareil"
       doi: "10.1128/msystems.00039-"
       licence: ["Artistic License 2.0"]
+      identifier: biotools:nonpareil
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test', single_end:false ]`
-  - npo:
-      type: file
-      description: Single npo redundancy summary file from nonpareil itself
-      pattern: "*.npo"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - npo:
+        type: file
+        description: Single npo redundancy summary file from nonpareil itself
+        pattern: "*.npo"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test', single_end:false ]`
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - png:
-      type: file
-      description: PNG file of the Nonpareil curve
-      pattern: "*.png"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.png":
+          type: file
+          description: PNG file of the Nonpareil curve
+          pattern: "*.png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@jfy133"
 maintainers:
diff --git a/nextflow.config b/nextflow.config
index e8dd7723..b972105c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,10 +13,6 @@ params {
 
     // Input options
     input                      = null
-    // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = false
 
     // MultiQC options
     multiqc_config             = null
@@ -34,30 +30,21 @@ 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/'
-    monochromeLogs               = false // required so nf-validation nextflow.enabled.strict works nicely together
-
-    // Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// 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,fasta,monochromeLogs'
-    validationShowHiddenParams       = false
-    validate_params                  = true
+    validate_params            = true
 
     // Databases
     databases               = null
@@ -200,20 +187,8 @@ 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: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load nf-core/taxprofiler custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
-}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
 
 profiles {
     debug {
@@ -229,7 +204,7 @@ 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 {
@@ -313,6 +288,13 @@ profiles {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
+        process {
+            resourceLimits = [
+                memory: 8.GB,
+                cpus  : 4,
+                time  : 1.h
+            ]
+        }
     }
     test                                 { includeConfig 'conf/test.config'                          }
     test_full                            { includeConfig 'conf/test_full.config'                     }
@@ -329,26 +311,23 @@ profiles {
     test_prinseqplusplus                 { includeConfig 'conf/test_prinseqplusplus.config'          }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
+// Load nf-core/taxprofiler custom profiles from different institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/taxprofiler.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'
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
 
-// Load igenomes.config if required
 
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
 // 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.
@@ -360,73 +339,126 @@ 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",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 
 manifest {
     name            = 'nf-core/taxprofiler'
-    author          = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team"""
+    author          = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        [
+            name: 'James A. Fellows Yates',
+            affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
+            email: 'jfy133@gmail.com',
+            github: 'https://github.com/jfy133',
+            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: 'https://orcid.org/0000-0001-5585-6277'
+        ],
+        [
+            name: 'Sofia Stamouli',
+            affiliation: 'Karolinska Institutet/Karolinska University Hospital/Clinical Genomics SciLifeLab, Solna, Sweden',
+            email: '',
+            github: 'https://github.com/sofstam',
+            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: 'https://orcid.org/0009-0006-0893-3771'
+        ],
+        [
+            name: 'Moritz E. Beber',
+            affiliation: 'Unseen Bio ApS, Copenhagen, Denmark​',
+            email: '',
+            github: 'https://github.com/Midnighter',
+            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: 'https://orcid.org/0000-0003-2406-1978'
+        ],
+        [
+            name: 'Lili Andersson-Li',
+            affiliation: 'Karolinska Institutet/Karolinska University Hospital/Clinical Genomics SciLifeLab, Solna, Sweden',
+            email: '',
+            github: 'https://github.com/LilyAnderssonLee',
+            contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: 'https://orcid.org/0000-0002-6059-4192'
+        ],
+        [
+            name: 'and the nf-core/taxprofiler team',
+            affiliation: 'nf-core community',
+            email: '',
+            github: 'https://github.com/nf-core',
+            contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+    ]
     homePage        = 'https://github.com/nf-core/taxprofiler'
     description     = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    defaultBranch   = 'master'
+    nextflowVersion = '!>=24.04.2'
     version         = '1.3.0dev'
     doi             = '10.1101/2023.10.20.563221'
 }
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.3.0' // 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 {
+    monochromeLogs = params.monochrome_logs
+    help {
+        enabled = true
+        command = "nextflow run nf-core/taxprofiler -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  nf-core/taxprofiler ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/nf-core/taxprofiler/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3ada1a56..499438c0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/taxprofiler/master/nextflow_schema.json",
     "title": "nf-core/taxprofiler pipeline parameters",
     "description": "Taxonomic classification and profiling of shotgun short- and long-read metagenomic data",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -675,32 +675,32 @@
                 },
                 "taxpasta_add_name": {
                     "type": "boolean",
-                    "description": "Add the taxon name to the output.",
-                    "help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon name can be added as additional information to the output table in addition to the taxon ID.\n\nModifies tool parameter(s):\n- taxpasta: `--add-name`",
+                    "description": "Add the taxon name to the output. Requires --taxpasta_taxonomy_dir.",
+                    "help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon name can be added as additional information to the output table in addition to the taxon ID. Requires --taxpasta_taxonomy_dir to be supplied to infer the additional information.\n\nModifies tool parameter(s):\n- taxpasta: `--add-name`",
                     "fa_icon": "fas fa-tag"
                 },
                 "taxpasta_add_rank": {
                     "type": "boolean",
-                    "description": "Add the taxon rank to the output.",
-                    "help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon rank of the given taxonomic entry can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank`",
+                    "description": "Add the taxon rank to the output. Requires --taxpasta_taxonomy_dir.",
+                    "help_text": "The standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon rank of the given taxonomic entry can be added as additional information to the output table. Requires --taxpasta_taxonomy_dir to be supplied to infer the additional information.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank`",
                     "fa_icon": "fas fa-sort-amount-down-alt"
                 },
                 "taxpasta_add_lineage": {
                     "type": "boolean",
-                    "description": "Add the taxon's entire name lineage to the output.",
-                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon names separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-lineage`\n",
+                    "description": "Add the taxon's entire name lineage to the output. Requires --taxpasta_taxonomy_dir.",
+                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon names separated by semi-colons can be added as additional information to the output table. Requires --taxpasta_taxonomy_dir to be supplied to infer the additional information.\n\nModifies tool parameter(s):\n- taxpasta: `--add-lineage`\n",
                     "fa_icon": "fas fa-link"
                 },
                 "taxpasta_add_idlineage": {
                     "type": "boolean",
-                    "description": "Add the taxon's entire ID lineage to the output.",
-                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon identifiers separated by semi-colons can be added as additional information to the output table.\n\nModifies tool parameter(s):\n- taxpasta: `--add-id-lineage`\n",
+                    "description": "Add the taxon's entire ID lineage to the output. Requires --taxpasta_taxonomy_dir.",
+                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxon's entire taxonomic lineage with the taxon identifiers separated by semi-colons can be added as additional information to the output table. Requires --taxpasta_taxonomy_dir to be supplied to infer the additional information.\n\nModifies tool parameter(s):\n- taxpasta: `--add-id-lineage`\n",
                     "fa_icon": "fas fa-link"
                 },
                 "taxpasta_add_ranklineage": {
                     "type": "boolean",
-                    "description": "Add the taxon's entire rank lineage to the output.",
-                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxonomic ranks categories of the taxon's entire lineage separated by semi-colons can be added as additional information to the output table. This complements `--taxpasta_add_lineage` by telling you which taxonomic rank level each entry in the lineage refers to.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank-lineage`\n",
+                    "description": "Add the taxon's entire rank lineage to the output. Requires --taxpasta_taxonomy_dir.",
+                    "help_text": "\nThe standard output format of taxpasta is a two-column table including the read counts and the integer taxonomic ID. The taxonomic ranks categories of the taxon's entire lineage separated by semi-colons can be added as additional information to the output table. This complements `--taxpasta_add_lineage` by telling you which taxonomic rank level each entry in the lineage refers to. Requires --taxpasta_taxonomy_dir to be supplied to infer the additional information.\n\nModifies tool parameter(s):\n- taxpasta: `--add-rank-lineage`\n",
                     "fa_icon": "fas fa-link"
                 },
                 "taxpasta_ignore_errors": {
@@ -760,41 +760,6 @@
                 }
             }
         },
-        "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",
@@ -802,12 +767,6 @@
             "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.",
@@ -883,106 +842,55 @@
                     "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",
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
-                }
-            }
-        },
-        "reference_genome_options": {
-            "title": "Reference genome options",
-            "type": "object",
-            "fa_icon": "fas fa-dna",
-            "description": "Reference genome related files and options required for the workflow.",
-            "properties": {
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
-                    "fa_icon": "fas fa-book",
-                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
-                    "hidden": true
                 },
-                "igenomes_base": {
+                "trace_report_suffix": {
                     "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes/",
-                    "fa_icon": "fas fa-cloud-download-alt",
+                    "fa_icon": "far calendar",
+                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
-                },
-                "igenomes_ignore": {
-                    "type": "boolean",
-                    "description": "Do not load the iGenomes reference config.",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                 }
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/preprocessing_general_qc_options"
-        },
-        {
-            "$ref": "#/definitions/preprocessing_short_read_qc_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/preprocessing_long_read_qc_options"
+            "$ref": "#/$defs/preprocessing_general_qc_options"
         },
         {
-            "$ref": "#/definitions/redundancy_estimation"
+            "$ref": "#/$defs/preprocessing_short_read_qc_options"
         },
         {
-            "$ref": "#/definitions/preprocessing_host_removal_options"
+            "$ref": "#/$defs/preprocessing_long_read_qc_options"
         },
         {
-            "$ref": "#/definitions/preprocessing_run_merging_options"
+            "$ref": "#/$defs/redundancy_estimation"
         },
         {
-            "$ref": "#/definitions/profiling_options"
+            "$ref": "#/$defs/preprocessing_host_removal_options"
         },
         {
-            "$ref": "#/definitions/postprocessing_and_visualisation_options"
+            "$ref": "#/$defs/preprocessing_run_merging_options"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/profiling_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/postprocessing_and_visualisation_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 00000000..c8a1f76d
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,364 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2025-01-27T14:48:54+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-taxprofiler_logo_custom_dark.png\">\n    <img alt=\"nf-core/taxprofiler\" src=\"docs/images/nf-core-taxprofiler_logo_custom_light.png.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/taxprofiler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n[![Cite Preprint](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://doi.org/10.1101/2023.10.20.563221)\n\n## Introduction\n\n**nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases.\n\n## Pipeline summary\n\n![](docs/images/taxprofiler_tube.png)\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`falco`](https://github.com/smithlabcode/falco) as an alternative option)\n2. Performs optional read pre-processing\n   - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop), [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI))\n   - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)), [Nanoq](https://github.com/esteinig/nanoq)\n   - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))\n   - Run merging\n3. Supports statistics metagenome coverage estimation ([Nonpareil](https://nonpareil.readthedocs.io/en/latest/)) and for host-read removal ([Samtools](http://www.htslib.org/))\n4. Performs taxonomic classification and/or profiling using one or more of:\n   - [Kraken2](https://ccb.jhu.edu/software/kraken2/)\n   - [MetaPhlAn](https://huttenhower.sph.harvard.edu/metaphlan/)\n   - [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/)\n   - [DIAMOND](https://github.com/bbuchfink/diamond)\n   - [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)\n   - [Kaiju](https://kaiju.binf.ku.dk/)\n   - [mOTUs](https://motu-tool.org/)\n   - [KrakenUniq](https://github.com/fbreitwieser/krakenuniq)\n   - [KMCP](https://github.com/shenwei356/kmcp)\n   - [ganon](https://pirovc.github.io/ganon/)\n5. Perform optional post-processing with:\n   - [bracken](https://ccb.jhu.edu/software/bracken/)\n6. Standardises output tables ([`Taxpasta`](https://taxpasta.readthedocs.io))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n8. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,run_accession,instrument_platform,fastq_1,fastq_2,fasta\n2612,run1,ILLUMINA,2612_run1_R1.fq.gz,,\n2612,run2,ILLUMINA,2612_run2_R1.fq.gz,,\n2612,run3,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz,\n```\n\nEach row represents a fastq file (single-end), a pair of fastq files (paired end), or a fasta (with long reads).\n\nAdditionally, you will need a database sheet that looks as follows:\n\n`databases.csv`:\n\n```csv\ntool,db_name,db_params,db_path\nkraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz\nmetaphlan,db1,,/<path>/<to>/metaphlan/metaphlan_database/\n```\n\nThat includes directories or `.tar.gz` archives containing databases for the tools you wish to run the pipeline against.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/taxprofiler \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --databases databases.csv \\\n   --outdir <OUTDIR>  \\\n   --run_kraken2 --run_metaphlan\n```\n\n> [!WARNING]\n> 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).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/taxprofiler/usage) and the [parameter documentation](https://nf-co.re/taxprofiler/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/taxprofiler/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/taxprofiler/output).\n\n## Credits\n\nnf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team.\n\n### Team\n\n- [James A. Fellows Yates](https://github.com/jfy133)\n- [Sofia Stamouli](https://github.com/sofstam)\n- [Moritz E. Beber](https://github.com/Midnighter)\n- [Lili Andersson-Li](https://github.com/LilyAnderssonLee)\n\nWe thank the following people for their contributions to the development of this pipeline:\n\n- [Lauri Mesilaakso](https://github.com/ljmesi)\n- [Tanja Normark](https://github.com/talnor)\n- [Maxime Borry](https://github.com/maxibor)\n- [Thomas A. Christensen II](https://github.com/MillironX)\n- [Jianhong Ou](https://github.com/jianhong)\n- [Rafal Stepien](https://github.com/rafalstepien)\n- [Mahwash Jamy](https://github.com/mjamy)\n\n### Acknowledgments\n\nWe also are grateful for the feedback and comments from:\n\n- The general [nf-core/community](https://nf-co.re/community)\n\nAnd specifically to\n\n- [Alex H\u00fcbner](https://github.com/alexhbnr)\n\n\u2764\ufe0f also goes to [Zandra Fagern\u00e4s](https://github.com/ZandraFagernas) for the logo.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#taxprofiler` channel](https://nfcore.slack.com/channels/taxprofiler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.1101/2023.10.20.563221](https://doi.org/10.1101/2023.10.20.563221).\n\n> Stamouli, S., Beber, M. E., Normark, T., Christensen II, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221\n\nFor the latest version of the code, cite the Zenodo doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "hasPart": [
+                {
+                    "@id": "main.nf"
+                },
+                {
+                    "@id": "assets/"
+                },
+                {
+                    "@id": "conf/"
+                },
+                {
+                    "@id": "docs/"
+                },
+                {
+                    "@id": "docs/images/"
+                },
+                {
+                    "@id": "modules/"
+                },
+                {
+                    "@id": "modules/local/"
+                },
+                {
+                    "@id": "modules/nf-core/"
+                },
+                {
+                    "@id": "workflows/"
+                },
+                {
+                    "@id": "subworkflows/"
+                },
+                {
+                    "@id": "nextflow.config"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "nextflow_schema.json"
+                },
+                {
+                    "@id": "CHANGELOG.md"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "CODE_OF_CONDUCT.md"
+                },
+                {
+                    "@id": "CITATIONS.md"
+                },
+                {
+                    "@id": "modules.json"
+                },
+                {
+                    "@id": "docs/usage.md"
+                },
+                {
+                    "@id": "docs/output.md"
+                },
+                {
+                    "@id": ".nf-core.yml"
+                },
+                {
+                    "@id": ".pre-commit-config.yaml"
+                },
+                {
+                    "@id": ".prettierignore"
+                }
+            ],
+            "isBasedOn": "https://github.com/nf-core/taxprofiler",
+            "license": "MIT",
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "mentions": [
+                {
+                    "@id": "#aa53606f-ee26-4042-9330-5732f42c26aa"
+                }
+            ],
+            "name": "nf-core/taxprofiler"
+        },
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                {
+                    "@id": "https://w3id.org/ro/crate/1.1"
+                },
+                {
+                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+                }
+            ]
+        },
+        {
+            "@id": "main.nf",
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "creator": [
+                {
+                    "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com"
+                },
+                {
+                    "@id": "#jfy133@gmail.com"
+                },
+                {
+                    "@id": "https://orcid.org/0009-0006-0893-3771"
+                },
+                {
+                    "@id": "#jfy133@gmail.com"
+                }
+            ],
+            "dateCreated": "",
+            "dateModified": "2025-01-27T14:48:54Z",
+            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "classification",
+                "illumina",
+                "long-reads",
+                "metagenomics",
+                "microbiome",
+                "nanopore",
+                "pathogen",
+                "profiling",
+                "shotgun",
+                "taxonomic-classification",
+                "taxonomic-profiling"
+            ],
+            "license": [
+                "MIT"
+            ],
+            "maintainer": [
+                {
+                    "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com"
+                },
+                {
+                    "@id": "#jfy133@gmail.com"
+                },
+                {
+                    "@id": "https://orcid.org/0009-0006-0893-3771"
+                }
+            ],
+            "name": [
+                "nf-core/taxprofiler"
+            ],
+            "programmingLanguage": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+            },
+            "sdPublisher": {
+                "@id": "https://nf-co.re/"
+            },
+            "url": ["https://github.com/nf-core/taxprofiler", "https://nf-co.re/taxprofiler/dev/"],
+            "version": ["1.3.0dev"]
+        },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+            "@type": "ComputerLanguage",
+            "identifier": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "name": "Nextflow",
+            "url": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "version": "!>=24.04.2"
+        },
+        {
+            "@id": "#aa53606f-ee26-4042-9330-5732f42c26aa",
+            "@type": "TestSuite",
+            "instance": [
+                {
+                    "@id": "#cb9bbf6a-2de4-481c-8f19-95a0367976ed"
+                }
+            ],
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "Test suite for nf-core/taxprofiler"
+        },
+        {
+            "@id": "#cb9bbf6a-2de4-481c-8f19-95a0367976ed",
+            "@type": "TestInstance",
+            "name": "GitHub Actions workflow for testing nf-core/taxprofiler",
+            "resource": "repos/nf-core/taxprofiler/actions/workflows/ci.yml",
+            "runsOn": {
+                "@id": "https://w3id.org/ro/terms/test#GithubService"
+            },
+            "url": "https://api.github.com"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#GithubService",
+            "@type": "TestService",
+            "name": "Github Actions",
+            "url": {
+                "@id": "https://github.com"
+            }
+        },
+        {
+            "@id": "assets/",
+            "@type": "Dataset",
+            "description": "Additional files"
+        },
+        {
+            "@id": "conf/",
+            "@type": "Dataset",
+            "description": "Configuration files"
+        },
+        {
+            "@id": "docs/",
+            "@type": "Dataset",
+            "description": "Markdown files for documenting the pipeline"
+        },
+        {
+            "@id": "docs/images/",
+            "@type": "Dataset",
+            "description": "Images for the documentation files"
+        },
+        {
+            "@id": "modules/",
+            "@type": "Dataset",
+            "description": "Modules used by the pipeline"
+        },
+        {
+            "@id": "modules/local/",
+            "@type": "Dataset",
+            "description": "Pipeline-specific modules"
+        },
+        {
+            "@id": "modules/nf-core/",
+            "@type": "Dataset",
+            "description": "nf-core modules"
+        },
+        {
+            "@id": "workflows/",
+            "@type": "Dataset",
+            "description": "Main pipeline workflows to be executed in main.nf"
+        },
+        {
+            "@id": "subworkflows/",
+            "@type": "Dataset",
+            "description": "Smaller subworkflows"
+        },
+        {
+            "@id": "nextflow.config",
+            "@type": "File",
+            "description": "Main Nextflow configuration file"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File",
+            "description": "Basic pipeline usage information"
+        },
+        {
+            "@id": "nextflow_schema.json",
+            "@type": "File",
+            "description": "JSON schema for pipeline parameter specification"
+        },
+        {
+            "@id": "CHANGELOG.md",
+            "@type": "File",
+            "description": "Information on changes made to the pipeline"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File",
+            "description": "The license - should be MIT"
+        },
+        {
+            "@id": "CODE_OF_CONDUCT.md",
+            "@type": "File",
+            "description": "The nf-core code of conduct"
+        },
+        {
+            "@id": "CITATIONS.md",
+            "@type": "File",
+            "description": "Citations needed when using the pipeline"
+        },
+        {
+            "@id": "modules.json",
+            "@type": "File",
+            "description": "Version information for modules from nf-core/modules"
+        },
+        {
+            "@id": "docs/usage.md",
+            "@type": "File",
+            "description": "Usage documentation"
+        },
+        {
+            "@id": "docs/output.md",
+            "@type": "File",
+            "description": "Output documentation"
+        },
+        {
+            "@id": ".nf-core.yml",
+            "@type": "File",
+            "description": "nf-core configuration file, configuring template features and linting rules"
+        },
+        {
+            "@id": ".pre-commit-config.yaml",
+            "@type": "File",
+            "description": "Configuration file for pre-commit hooks"
+        },
+        {
+            "@id": ".prettierignore",
+            "@type": "File",
+            "description": "Ignore file for prettier"
+        },
+        {
+            "@id": "https://nf-co.re/",
+            "@type": "Organization",
+            "name": "nf-core",
+            "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com",
+            "@type": "Person",
+            "email": "64467552+LilyAnderssonLee@users.noreply.github.com",
+            "name": "Lili Andersson-Li"
+        },
+        {
+            "@id": "#jfy133@gmail.com",
+            "@type": "Person",
+            "email": "jfy133@gmail.com",
+            "name": "James Fellows Yates"
+        },
+        {
+            "@id": "https://orcid.org/0009-0006-0893-3771",
+            "@type": "Person",
+            "email": "91951607+sofstam@users.noreply.github.com",
+            "name": "Sofia Stamouli"
+        }
+    ]
+}
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 8b38baca..e21a745b 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -388,16 +388,24 @@ workflow PROFILING {
             .map {
                 meta, reads, db_meta, db ->
                     def seqtype = (reads[0].name ==~ /.+?\.f\w{0,3}a(\.gz)?$/) ? 'fasta' : 'fastq'
-                    [[id: db_meta.db_name, single_end: meta.single_end, seqtype: seqtype], reads, db_meta, db]
+                    // We bundle the sample identifier with the sequencing files to undergo batching.
+                    def prefix = params.perform_runmerging ? meta.id : "${meta.id}_${meta.run_accession}"
+                    prefix = meta.single_end ? "${prefix}.se" : "${prefix}.pe"
+                    [[id: db_meta.db_name, single_end: meta.single_end, seqtype: seqtype], reads + [prefix], db_meta, db]
             }
             .groupTuple(by: [0,2,3])
             .flatMap { single_meta, reads, db_meta, db ->
                 def batches = reads.collate(params.krakenuniq_batch_size)
-                return batches.collect { batch -> [ single_meta + db_meta, batch.flatten(), db ]}
+                return batches.collect { batch ->
+                    // We split the sample identifier from the reads again after batching.
+                    def reads_batch = batch.collect { elements -> elements.take(elements.size() - 1) }.flatten()
+                    def prefixes = batch.collect { elements -> elements[-1] }
+                    return [ single_meta + db_meta, reads_batch, prefixes, db ]
+                }
             }
             .multiMap {
-                meta, reads, db ->
-                    reads: [ meta, reads ]
+                meta, reads, prefixes, db ->
+                    reads: [ meta, reads, prefixes ]
                     db: db
                     seqtype: meta.seqtype
             }
diff --git a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf b/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf
index 9b4f6df5..7e4f255c 100644
--- a/subworkflows/local/utils_nfcore_taxprofiler_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_taxprofiler_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
@@ -55,16 +51,10 @@ 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 --databases databases.csv --outdir <OUTDIR> --run_kraken2"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        "nextflow_schema.json"
+        null
     )
 
     //
@@ -73,23 +63,20 @@ workflow PIPELINE_INITIALISATION {
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
-    //
-    // Custom validation for pipeline parameters
-    //
-    validateInputParameters()
 
     //
     // Create channel from input file provided through params.input
     //
+
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "assets/schema_input.json"))
         .set { ch_samplesheet }
 
     //
     // Create channel from databases file provided through params.databases
     //
     Channel
-        .fromSamplesheet("databases")
+        .fromList(samplesheetToList(params.databases, "assets/schema_database.json"))
         .set {ch_databases}
 
     emit:
@@ -99,9 +86,9 @@ workflow PIPELINE_INITIALISATION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -116,19 +103,26 @@ workflow PIPELINE_COMPLETION {
     multiqc_report  //  string: Path to MultiQC report
 
     main:
-
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    def multiqc_reports = multiqc_report.toList()
 
     //
     // Completion email and summary
     //
     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_reports.getVal(),
+            )
         }
 
         completionSummary(monochrome_logs)
-
         if (hook_url) {
             imNotification(summary_params, hook_url)
         }
@@ -140,54 +134,25 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-//
-// Check and validate pipeline parameters
-//
-def validateInputParameters() {
-    genomeExistsError()
-}//
 // Validate channels from input samplesheet
 //
 def validateInputSamplesheet(input) {
     def (metas, fastqs, fasta) = input[1..3]
 
     // 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}")
     }
 
     return [ metas[0], fastqs, fasta ]
 }
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
 
 //
-// Exit pipeline if incorrect --genome key provided
-//
-def genomeExistsError() {
-    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-            "  Currently, the available genome keys are:\n" +
-            "  ${params.genomes.keySet().join(", ")}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        error(error_string)
-    }
-}//
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
@@ -357,8 +322,8 @@ def toolBibliographyText() {
     return reference_text
 }
 
-def methodsDescriptionText( mqc_methods_yaml ) {
-
+def methodsDescriptionText(mqc_methods_yaml) {
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
 
     meta.workflow = workflow.toMap()
@@ -370,8 +335,10 @@ 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>"
@@ -389,3 +356,4 @@ def methodsDescriptionText( mqc_methods_yaml ) {
 
     return description_html.toString()
 }
+
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 28e32b20..d6e593e8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NEXTFLOW_PIPELINE {
-
     take:
     print_version        // boolean: print version
     dump_parameters      // boolean: dump parameters
@@ -22,7 +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)
     }
 
@@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -72,11 +71,11 @@ 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    = groovy.json.JsonOutput.toJson(params)
-    temp_pf.text   = groovy.json.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)
 
     nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
@@ -91,9 +90,16 @@ def checkCondaChannels() {
     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.debug(e)
+        log.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.debug(e)
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -102,23 +108,19 @@ def checkCondaChannels() {
     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
-
-    required_channels_in_order.eachWithIndex { channel, index ->
-        if (index < required_channels_in_order.size() - 1) {
-            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
-        }
-    }
+    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/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index cbd8495b..bfd25876 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -3,13 +3,12 @@
 //
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW DEFINITION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow UTILS_NFCORE_PIPELINE {
-
     take:
     nextflow_cli_args
 
@@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE {
 def checkConfigProvided() {
     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
@@ -49,34 +45,15 @@ 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 `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
-    }
-}
-
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Using a loop to handle multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    manifest_doi.each { doi_ref ->
-        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\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"
+        )
     }
-    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"
 }
 
 //
@@ -102,7 +79,7 @@ def getWorkflowVersion() {
 //
 def processVersionsFromYAML(yaml_file) {
     def yaml = new org.yaml.snakeyaml.Yaml()
-    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -112,8 +89,8 @@ 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()
 }
 
@@ -121,11 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,56 +106,35 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    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>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${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"
         }
-    }
 
-    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}"
+    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
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
@@ -199,79 +151,76 @@ 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
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
-                }
-                mqc_report = mqc_report[0]
-            }
-        }
-    } catch (all) {
-        if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    return mqc_report
 }
 
 //
@@ -280,26 +229,35 @@ 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 = [:]
-    summary_params.keySet().sort().each { group ->
-        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 = [:]
@@ -316,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -336,8 +294,8 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // 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: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +304,35 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${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 ${email_address} (sendmail)-")
+        }
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${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 }
-    nextflow.extension.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 }
-    nextflow.extension.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()
 }
 
@@ -380,12 +343,14 @@ def completionSummary(monochrome_logs=true) {
     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}-")
     }
 }
 
@@ -394,21 +359,30 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    summary_params.keySet().sort().each { group ->
-        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()
@@ -433,13 +407,13 @@ 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_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f8..f117040c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232c..02c67014 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
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 00000000..4994303e
--- /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 00000000..f7d9f028
--- /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 00000000..8fb30164
--- /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      = null
+            }
+
+            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] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = null
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${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 00000000..0907ac58
--- /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 = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c9..331e0d2f 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$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 2585b65d..00000000
--- 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 3d4a6b04..00000000
--- 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 5784a33f..00000000
--- 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 60b1cfff..00000000
--- 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/taxprofiler.nf b/workflows/taxprofiler.nf
index 93eb55dd..5a1aac03 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -3,17 +3,15 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { FASTQC                 } from '../modules/nf-core/fastqc/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap       } from 'plugin/nf-validation'
+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_taxprofiler_pipeline'
-include { validateParameters; paramsHelp; paramsSummaryLog; fromSamplesheet } from 'plugin/nf-validation'
 
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.genome, params.databases,
+def checkPathParamList = [ params.input, params.databases,
                             params.longread_hostremoval_index,
                             params.hostremoval_reference, params.shortread_hostremoval_index,
                             params.multiqc_config, params.shortread_qc_adapterlist,
@@ -334,11 +332,12 @@ workflow TAXPROFILER {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            name: 'nf_core_'  +  'taxprofiler_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }
 
+
     //
     // MODULE: MultiQC
     //
@@ -354,15 +353,14 @@ workflow TAXPROFILER {
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
     ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
-
+    ch_multiqc_files = ch_multiqc_files.mix(
+        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_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_methods_description.collectFile(
@@ -423,9 +421,9 @@ workflow TAXPROFILER {
         []
     )
 
-    emit:
-    multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+    emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
     versions       = ch_versions                 // channel: [ path(versions.yml) ]
+
 }
 
 /*