diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index d784a8bbc..f2e9f3318 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/rnaseq, the standard workflow is as
 1. Check that there isn't already an issue about your idea in the [nf-core/rnaseq issues](https://github.com/nf-core/rnaseq/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/rnaseq repository](https://github.com/nf-core/rnaseq) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -40,7 +40,7 @@ There are typically two types of tests that run:
 ### Lint tests
 
 `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
+To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
@@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### Nextflow version bumping
 
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
+If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
 
 ### Images and figures
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 5ed2fd931..3473f145d 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/rnas
 - [ ] 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/rnaseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/rnaseq _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/ci.yml b/.github/workflows/ci.yml
index 8346f837c..ef022099b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -2,13 +2,16 @@ name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
 env:
-  NXF_ANSI_LOG: false
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
   NFT_VER: "0.9.0"
   NFT_WORKDIR: "~"
-  NFT_DIFF: "pdiff"
-  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  NXF_ANSI_LOG: false
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -45,8 +48,8 @@ jobs:
       fail-fast: false
       matrix:
         NXF_VER:
+          - "24.04.2"
           - "latest-everything"
-          - "23.04"
         nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
@@ -60,6 +63,11 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
       - uses: actions/setup-python@v4
         with:
           python-version: "3.11"
@@ -70,8 +78,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install pdiff
 
-      - uses: nf-core/setup-nf-test@v1
-
       - name: Run nf-test
         run: |
           nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2d20d6442..713dc3e73 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -1,4 +1,4 @@
-name: Test successful pipeline download with 'nf-core download'
+name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       testbranch:
-        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download."
         required: true
         default: "dev"
   pull_request:
@@ -39,9 +39,11 @@ jobs:
         with:
           python-version: "3.12"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+
+      - name: Setup Apptainer
+        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.4
 
       - name: Install dependencies
         run: |
@@ -54,33 +56,64 @@ jobs:
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
           echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
+      - name: Make a cache directory for the container images
+        run: |
+          mkdir -p ./singularity_container_images
+
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core download ${{ env.REPO_LOWERCASE }} \
+          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "ghcr.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
           --container-cache-utilisation 'amend' \
-          --download-configuration
+          --download-configuration 'yes'
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
+      - name: Count the downloaded number of container images
+        id: count_initial
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Initial container image count: $image_count"
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
-          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+
+      - name: Count the downloaded number of container images
+        id: count_afterwards
+        run: |
+          image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
+          echo "Post-pipeline run container image count: $image_count"
+          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+
+      - name: Compare container image counts
+        run: |
+          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
+            final_count=${{ env.IMAGE_COUNT_AFTER }}
+            difference=$((final_count - initial_count))
+            echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
+            tree ./singularity_container_images
+            exit 1
+          else
+            echo "The pipeline can be downloaded successfully!"
+          fi
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 1fcafe880..a502573c5 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,6 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure
+# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
   push:
@@ -41,17 +41,32 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.1.0
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Run nf-core pipelines lint
+        if: ${{ github.base_ref != 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 40acc23f5..42e519bfa 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 03ecfcf72..c6ba35df4 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
new file mode 100644
index 000000000..9dea41f0d
--- /dev/null
+++ b/.github/workflows/template_version_comment.yml
@@ -0,0 +1,43 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Read template version from .nf-core.yml
+        uses: pietrobolcato/action-read-yaml@1.0.0
+        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: pip list --outdated | grep nf-core
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          ${{ steps.nf_core_outdated.outputs.stdout }} =~ '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/.gitpod.yml b/.gitpod.yml
index 105a1821a..461186376 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -4,17 +4,14 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-  - name: unset JAVA_TOOL_OPTIONS
-    command: |
-      unset JAVA_TOOL_OPTIONS
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                    # Nextflow syntax highlighting
+    - nextflow.nextflow # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
     - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index d01e0a8b4..15806017b 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,15 +1,29 @@
-repository_type: pipeline
-nf_core_version: "2.14.1"
+bump_version: null
 lint:
+  actions_ci: false
+  files_exist:
+    - conf/modules.config
   files_unchanged:
     - assets/email_template.html
     - assets/email_template.txt
     - .gitignore
-  files_exist:
-    - conf/modules.config
-  actions_ci: false
-  multiqc_config: false
   modules_config: false
+  multiqc_config: false
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
+nf_core_version: 3.0.1
+org_path: null
+repository_type: pipeline
+template:
+  author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
+  description: RNA sequencing analysis pipeline for gene/isoform quantification and
+    extensive quality control.
+  force: false
+  is_nfcore: true
+  name: rnaseq
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 3.17.0dev
+update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4dc0f1dcd..9e9f0e1c4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "2.7.3"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 669cd30f2..7d45d8e28 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,14 +7,45 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Credits
 
+Special thanks to the following for their contributions to the release:
+
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+
 ### Enhancements & fixes
 
 - [PR #1398](https://github.com/nf-core/rnaseq/pull/1398) - Bump pipeline version to 3.17.0dev
+- [PR #1401](https://github.com/nf-core/rnaseq/pull/1401) - Template update for nf-core/tools v3.0.1
 
 ### Parameters
 
+| Old parameter                        | New parameter   |
+| ------------------------------------ | --------------- |
+|                                      | `--help_full`   |
+|                                      | `--show_hidden` |
+| `--validationFailUnrecognisedParams` |                 |
+| `--validationLenientMode`            |                 |
+| `--validationSchemaIgnoreParams`     |                 |
+| `--validationShowHiddenParams`       |                 |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present.
+>
+> **NB:** Parameter has been **added** if just the new parameter information is present.
+>
+> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ### Software dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `MultiQC`  | 1.24.1      | 1.25.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[3.16.0](https://github.com/nf-core/rnaseq/releases/tag/3.16.0)] - 2024-10-02
 
 ### Credits
@@ -58,8 +89,8 @@ Special thanks to the following for their contributions to the release:
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| `Kraken2`  | ----------- | 2.1.3       |
-| `Bracken`  | ----------- | 2.9         |
+| `Kraken2`  |             | 2.1.3       |
+| `Bracken`  |             | 2.9         |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
 >
diff --git a/README.md b/README.md
index 01da6cf8b..551cb7fb5 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@
 [![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/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/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)[![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/)
@@ -91,8 +91,7 @@ nextflow run nf-core/rnaseq \
 ```
 
 > [!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/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 1af6309dd..e6de3c264 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/rnaseq/master/assets/schema_input.json",
     "title": "nf-core/rnaseq pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
diff --git a/conf/base.config b/conf/base.config
index 93ad25b28..11d50feaf 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,9 +10,10 @@
 
 process {
 
-    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+    // TODO nf-core: Check the defaults for all processes
+    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
@@ -25,30 +26,30 @@ process {
     //        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( 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 }
     }
     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'
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
new file mode 100644
index 000000000..b4034d824
--- /dev/null
+++ b/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/conf/test.config b/conf/test.config
index f7a9fca91..153200306 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,15 +10,18 @@
 ----------------------------------------------------------------------------------------
 */
 
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
-
     // Input data
     input              = 'https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv'
 
diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png
deleted file mode 100755
index 361d0e47a..000000000
Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ
diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png
deleted file mode 100755
index cb39ebb80..000000000
Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ
diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png
deleted file mode 100755
index a4b89bf56..000000000
Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ
diff --git a/docs/output.md b/docs/output.md
index fe3757ad7..ca828e9fc 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -14,40 +14,50 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [Preprocessing](#preprocessing)
-  - [cat](#cat) - Merge re-sequenced FastQ files
-  - [FastQC](#fastqc) - Raw read QC
-  - [UMI-tools extract](#umi-tools-extract) - UMI barcode extraction
-  - [TrimGalore](#trimgalore) - Adapter and quality trimming
-  - [fastp](#fastp) - Adapter and quality trimming
-  - [BBSplit](#bbsplit) - Removal of genome contaminants
-  - [SortMeRNA](#sortmerna) - Removal of ribosomal RNA
-- [Alignment and quantification](#alignment-and-quantification)
-  - [STAR and Salmon](#star-and-salmon) - Fast spliced aware genome alignment and transcriptome quantification
-  - [STAR via RSEM](#star-via-rsem) - Alignment and quantification of expression levels
-  - [HISAT2](#hisat2) - Memory efficient splice aware alignment to a reference
-- [Alignment post-processing](#alignment-post-processing)
-  - [SAMtools](#samtools) - Sort and index alignments
-  - [UMI-tools dedup](#umi-tools-dedup) - UMI-based deduplication
-  - [picard MarkDuplicates](#picard-markduplicates) - Duplicate read marking
-- [Other steps](#other-steps)
-  - [StringTie](#stringtie) - Transcript assembly and quantification
-  - [BEDTools and bedGraphToBigWig](#bedtools-and-bedgraphtobigwig) - Create bigWig coverage files
-- [Quality control](#quality-control)
-  - [RSeQC](#rseqc) - Various RNA-seq QC metrics
-  - [Qualimap](#qualimap) - Various RNA-seq QC metrics
-  - [dupRadar](#dupradar) - Assessment of technical / biological read duplication
-  - [Preseq](#preseq) - Estimation of library complexity
-  - [featureCounts](#featurecounts) - Read counting relative to gene biotype
-  - [DESeq2](#deseq2) - PCA plot and sample pairwise distance heatmap and dendrogram
-  - [Kraken2/Bracken](#kraken2bracken) - Taxonomic classification of unaligned reads
-  - [MultiQC](#multiqc) - Present QC for raw reads, alignment, read counting and sample similiarity
-- [Pseudoalignment and quantification](#pseudoalignment-and-quantification)
-  - [Salmon](#pseudoalignment) - Wicked fast gene and isoform quantification relative to the transcriptome
-  - [Kallisto](#pseudoalignment) - Near-optimal probabilistic RNA-seq quantification
-- [Workflow reporting and genomes](#workflow-reporting-and-genomes)
-  - [Reference genome files](#reference-genome-files) - Saving reference genome indices/files
-  - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [nf-core/rnaseq: Output](#nf-corernaseq-output)
+  - [Introduction](#introduction)
+  - [Pipeline overview](#pipeline-overview)
+  - [Preprocessing](#preprocessing)
+    - [cat](#cat)
+    - [FastQC](#fastqc)
+    - [UMI-tools extract](#umi-tools-extract)
+    - [TrimGalore](#trimgalore)
+    - [fastp](#fastp)
+    - [BBSplit](#bbsplit)
+    - [SortMeRNA](#sortmerna)
+  - [Alignment and quantification](#alignment-and-quantification)
+    - [STAR, Salmon and Kallisto](#star-salmon-and-kallisto)
+    - [STAR via RSEM](#star-via-rsem)
+    - [HISAT2](#hisat2)
+  - [Alignment post-processing](#alignment-post-processing)
+    - [SAMtools](#samtools)
+    - [UMI-tools dedup](#umi-tools-dedup)
+    - [picard MarkDuplicates](#picard-markduplicates)
+  - [Other steps](#other-steps)
+    - [StringTie](#stringtie)
+    - [BEDTools and bedGraphToBigWig](#bedtools-and-bedgraphtobigwig)
+  - [Quality control](#quality-control)
+    - [RSeQC](#rseqc)
+      - [Infer experiment](#infer-experiment)
+      - [Read distribution](#read-distribution)
+      - [Junction annotation](#junction-annotation)
+      - [Inner distance](#inner-distance)
+      - [Junction saturation](#junction-saturation)
+      - [Read duplication](#read-duplication)
+      - [BAM stat](#bam-stat)
+      - [TIN](#tin)
+    - [Qualimap](#qualimap)
+    - [dupRadar](#dupradar)
+    - [Preseq](#preseq)
+    - [featureCounts](#featurecounts)
+    - [DESeq2](#deseq2)
+    - [Kraken2/Bracken](#kraken2bracken)
+    - [MultiQC](#multiqc)
+  - [Pseudoalignment and quantification](#pseudoalignment-and-quantification)
+    - [Pseudoalignment](#pseudoalignment)
+  - [Workflow reporting and genomes](#workflow-reporting-and-genomes)
+    - [Reference genome files](#reference-genome-files)
+    - [Pipeline information](#pipeline-information)
 
 ## Preprocessing
 
diff --git a/docs/usage.md b/docs/usage.md
index cd42a399b..ad2aa4e26 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -345,7 +345,7 @@ The above pipeline run specified with a params file in yaml format:
 nextflow run nf-core/rnaseq -profile docker -params-file params.yaml
 ```
 
-with `params.yaml` containing:
+with:
 
 ```yaml
 input: <SAMPLESHEET>
diff --git a/main.nf b/main.nf
index a0a6f1c7d..74599c9f0 100755
--- a/main.nf
+++ b/main.nf
@@ -9,8 +9,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-nextflow.enable.dsl = 2
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     GENOME PARAMETER VALUES
@@ -141,14 +139,11 @@ workflow NFCORE_RNASEQ {
 workflow {
 
     main:
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
     PIPELINE_INITIALISATION (
         params.version,
-        params.help,
-        "nextflow_schema.json",
         params.validate_params,
         params.monochrome_logs,
         args,
@@ -164,7 +159,6 @@ workflow {
     // SUBWORKFLOW: Run completion tasks
     //
     PIPELINE_COMPLETION (
-        "nextflow_schema.json",
         params.email,
         params.email_on_fail,
         params.plaintext_email,
diff --git a/modules.json b/modules.json
index c351786e2..f4460822d 100644
--- a/modules.json
+++ b/modules.json
@@ -53,7 +53,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "fq/subsample": {
@@ -104,7 +104,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -244,7 +244,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "tximeta/tximport": {
@@ -269,7 +269,7 @@
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "umitools/prepareforrsem": {
@@ -332,7 +332,7 @@
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
+                        "git_sha": "53fcc37e256ea30818fb793bbe98b63e4a40deb8",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
                     },
                     "fastq_qc_trim_filter_setstrandedness": {
@@ -352,17 +352,17 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/bracken/bracken/tests/tags.yml b/modules/nf-core/bracken/bracken/tests/tags.yml
deleted file mode 100644
index 6a2cbd384..000000000
--- a/modules/nf-core/bracken/bracken/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bracken/bracken:
-  - "modules/nf-core/bracken/bracken/**"
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index ee5507e06..4827da7af 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/kraken2/kraken2/tests/tags.yml b/modules/nf-core/kraken2/kraken2/tests/tags.yml
deleted file mode 100644
index 9ebfd7ab6..000000000
--- a/modules/nf-core/kraken2/kraken2/tests/tags.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-kraken2/kraken2:
-  - modules/nf-core/kraken2/kraken2/**
-  - modules/nf-core/untar/**
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index f1cd99b07..6f5b867b7 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=1.24.1
+  - bioconda::multiqc=1.25.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index ceaec139e..9724d2f34 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:1.24.1--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 382c08cbc..b16c18792 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,53 +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 83fa080c8..2fcbb5ff7 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T12:41:34.562023"
+        "timestamp": "2024-10-02T17:51:46.317523"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:27:11.933869532"
+        "timestamp": "2024-10-02T17:52:20.680978"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
+                "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-10T11:26:56.709849369"
+        "timestamp": "2024-10-02T17:52:09.185842"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml
index e649088ce..576cb4c59 100644
--- a/modules/nf-core/trimgalore/meta.yml
+++ b/modules/nf-core/trimgalore/meta.yml
@@ -14,50 +14,77 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
       documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
       licence: ["GPL-3.0-or-later"]
+      identifier: ""
 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 ]
   - reads:
-      type: file
-      description: |
-        List of input adapter trimmed FastQ files of size 1 and 2 for
-        single-end and paired-end data, respectively.
-      pattern: "*{3prime,5prime,trimmed,val}*.fq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*{3prime,5prime,trimmed,val}*.fq.gz":
+          type: file
+          description: |
+            List of input adapter trimmed FastQ files of size 1 and 2 for
+            single-end and paired-end data, respectively.
+          pattern: "*{3prime,5prime,trimmed,val}*.fq.gz"
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*report.txt":
+          type: file
+          description: Trim Galore! trimming report
+          pattern: "*_{report.txt}"
   - unpaired:
-      type: file
-      description: |
-        FastQ files containing unpaired reads from read 1 or read 2
-      pattern: "*unpaired*.fq.gz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*unpaired*.fq.gz":
+          type: file
+          description: |
+            FastQ files containing unpaired reads from read 1 or read 2
+          pattern: "*unpaired*.fq.gz"
   - html:
-      type: file
-      description: FastQC report (optional)
-      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 (optional)
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive (optional)
-      pattern: "*_{fastqc.zip}"
-  - log:
-      type: file
-      description: Trim Galore! trimming report
-      pattern: "*_{report.txt}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive (optional)
+          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"
   - "@ewels"
diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml
index 7695b2717..648ffbd26 100644
--- a/modules/nf-core/umitools/extract/meta.yml
+++ b/modules/nf-core/umitools/extract/meta.yml
@@ -1,5 +1,6 @@
 name: umitools_extract
-description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place
+description: Extracts UMI barcode from a read and add it to the read name, leaving
+  any sample barcode in place
 keywords:
   - UMI
   - barcode
@@ -8,38 +9,49 @@ keywords:
 tools:
   - umi_tools:
       description: >
-        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
+        UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random
+        Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes
       documentation: https://umi-tools.readthedocs.io/en/latest/
       license: "MIT"
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: list
-      description: |
-        List of input FASTQ files whose UMIs will be extracted.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: list
+        description: |
+          List of input FASTQ files whose UMIs will be extracted.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - reads:
-      type: file
-      description: >
-        Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
-      pattern: "*.{fastq.gz}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.fastq.gz":
+          type: file
+          description: >
+            Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz.
+            | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz.
+          pattern: "*.{fastq.gz}"
   - log:
-      type: file
-      description: Logfile for umi_tools
-      pattern: "*.{log}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.log":
+          type: file
+          description: Logfile for umi_tools
+          pattern: "*.{log}"
   - 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/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test
index 3eec566be..fc90a7a06 100644
--- a/modules/nf-core/umitools/extract/tests/main.nf.test
+++ b/modules/nf-core/umitools/extract/tests/main.nf.test
@@ -4,7 +4,6 @@ nextflow_process {
     script "../main.nf"
     process "UMITOOLS_EXTRACT"
     config "./nextflow.config"
-
     test("single end") {
 
         when {
diff --git a/nextflow.config b/nextflow.config
index fe4d8d28f..0c225476d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -117,30 +117,22 @@ params {
     monochrome_logs              = false
     hook_url                     = null
     help                         = false
+    help_full                    = false
+    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/'
 
     // Config options
     config_profile_name        = null
     config_profile_description = null
+
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
 
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
     // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
-
+    validate_params            = true
 }
 
 // Default publishing logic for pipeline
@@ -155,20 +147,6 @@ process {
 // 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: ${params.custom_config_base}/nfcore_custom.config")
-}
-
-// Load nf-core/rnaseq custom profiles from different institutions.
-try {
-    includeConfig "${params.custom_config_base}/pipeline/rnaseq.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config/rnaseq profiles: ${params.custom_config_base}/pipeline/rnaseq.config")
-}
-
 profiles {
     debug {
         dumpHashes              = true
@@ -183,7 +161,7 @@ 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 {
@@ -283,25 +261,23 @@ profiles {
     }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+// Load nf-core custom profiles from different Institutions
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Nextflow plugins
-plugins {
-    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
+// Load nf-core/rnaseq custom profiles from different institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnaseq.config" : "/dev/null"
+
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
+includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
@@ -314,8 +290,14 @@ env {
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
 }
 
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
+// Set bash options
+process.shell = """\
+bash
+
+set -e # Exit if a tool returns a non-zero status/exit code
+set -u # Treat unset variables and parameters as an error
+set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+"""
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -344,44 +326,47 @@ manifest {
     homePage        = 'https://github.com/nf-core/rnaseq'
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
     version         = '3.17.0dev'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 
-// Workflow specific config
-includeConfig "./subworkflows/local/prepare_genome/nextflow.config"
-includeConfig './workflows/rnaseq/nextflow.config'
+// Nextflow plugins
+plugins {
+    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
-        }
+validation {
+    defaultIgnoreParams = ["genomes"]
+    help {
+        enabled = true
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+-\033[2m----------------------------------------------------\033[0m-
+                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
+\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
+\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
+\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
+                                        \033[0;32m`._,._,\'\033[0m
+\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+-\033[2m----------------------------------------------------\033[0m-
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* The nf-core framework
+    https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+    }
+    summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
     }
 }
+
+// Load DSL2 module specific options
+includeConfig "./subworkflows/local/prepare_genome/nextflow.config"
+includeConfig './workflows/rnaseq/nextflow.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e7cd6d468..802209b42 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",
     "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/nextflow_schema.json",
     "title": "nf-core/rnaseq pipeline parameters",
     "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -196,20 +196,20 @@
                     "fa_icon": "fas fa-indent",
                     "help_text": "The feature type used from the GTF file when generating the biotype plot with featureCounts."
                 },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes/",
-                    "fa_icon": "fas fa-cloud-download-alt",
-                    "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`."
+                },
+                "igenomes_base": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             }
         },
@@ -729,41 +729,6 @@
                 }
             }
         },
-        "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",
@@ -771,12 +736,6 @@
             "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.",
@@ -859,27 +818,6 @@
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },
-                "validationShowHiddenParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-eye-slash",
-                    "description": "Show all params when using `--help`",
-                    "hidden": true,
-                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
-                },
-                "validationFailUnrecognisedParams": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "hidden": true,
-                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
-                },
-                "validationLenientMode": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-check-circle",
-                    "description": "Validation of parameters in lenient more.",
-                    "hidden": true,
-                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
-                },
                 "pipelines_testdata_base_path": {
                     "type": "string",
                     "fa_icon": "far fa-check-circle",
@@ -892,40 +830,37 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
-        },
-        {
-            "$ref": "#/definitions/reference_genome_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/read_trimming_options"
+            "$ref": "#/$defs/reference_genome_options"
         },
         {
-            "$ref": "#/definitions/read_filtering_options"
+            "$ref": "#/$defs/read_trimming_options"
         },
         {
-            "$ref": "#/definitions/umi_options"
+            "$ref": "#/$defs/read_filtering_options"
         },
         {
-            "$ref": "#/definitions/alignment_options"
+            "$ref": "#/$defs/umi_options"
         },
         {
-            "$ref": "#/definitions/optional_outputs"
+            "$ref": "#/$defs/alignment_options"
         },
         {
-            "$ref": "#/definitions/quality_control"
+            "$ref": "#/$defs/optional_outputs"
         },
         {
-            "$ref": "#/definitions/process_skipping_options"
+            "$ref": "#/$defs/quality_control"
         },
         {
-            "$ref": "#/definitions/institutional_config_options"
+            "$ref": "#/$defs/process_skipping_options"
         },
         {
-            "$ref": "#/definitions/max_job_request_options"
+            "$ref": "#/$defs/institutional_config_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/nf-test.config b/nf-test.config
index c843dabec..9069ed831 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -12,7 +12,7 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-bam@0.3.0"
-        load "nft-utils@0.0.2"
+        load "nft-bam@0.4.0"
+        load "nft-utils@0.0.3"
     }
 }
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
index cb051a38c..2aa411a68 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -10,37 +10,36 @@ import groovy.json.JsonSlurper
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
-include { paramsSummaryMap          } 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 { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
-include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } 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'
 include { logColours                } from '../../nf-core/utils_nfcore_pipeline'
 include { calculateStrandedness     } from '../../nf-core/fastq_qc_trim_filter_setstrandedness'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
 
     take:
     version           // boolean: Display version and exit
-    help              // boolean: Display help text
-    schema            //  string: Path to the JSON schema file
     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
+    nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
 
     main:
 
+    ch_versions = Channel.empty()
+
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
@@ -51,21 +50,17 @@ workflow PIPELINE_INITIALISATION {
         workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
     )
 
+
     //
     // 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 --genome GRCh37 --outdir <OUTDIR>"
-    UTILS_NFVALIDATION_PLUGIN (
-        help,
-        workflow_command,
-        pre_help_text,
-        post_help_text,
+    UTILS_NFSCHEMA_PLUGIN (
+        workflow,
         validate_params,
-        schema
+        null
     )
 
+
     //
     // Check config provided to the pipeline
     //
@@ -78,12 +73,35 @@ workflow PIPELINE_INITIALISATION {
     //
     validateInputParameters()
 
+    //
+    // Create channel from input file provided through params.input
+    //
+
+    Channel
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .map {
+            meta, fastq_1, fastq_2 ->
+                if (!fastq_2) {
+                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
+                } else {
+                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
+                }
+        }
+        .groupTuple()
+        .map {
+            checkSamplesAfterGrouping(it)
+        }
+        .set{ ch_samplesheet }
+
+    emit:
+    samplesheet = ch_samplesheet
+    versions    = ch_versions
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 def pass_mapped_reads  = [:]
@@ -93,21 +111,20 @@ def pass_strand_check  = [:]
 workflow PIPELINE_COMPLETION {
 
     take:
-    schema             //  string: Path to the JSON schema file
-    email              //  string: email address
-    email_on_fail      //  string: email address sent on pipeline failure
-    plaintext_email    // boolean: Send plain-text email instead of HTML
-    outdir             //    path: Path to output directory where results will be published
-    monochrome_logs    // boolean: Disable ANSI colour codes in log output
-    hook_url           //  string: hook URL for notifications
-    multiqc_report     //  string: Path to MultiQC report
+    email           //  string: email address
+    email_on_fail   //  string: email address sent on pipeline failure
+    plaintext_email // boolean: Send plain-text email instead of HTML
+
+    outdir          //    path: Path to output directory where results will be published
+    monochrome_logs // boolean: Disable ANSI colour codes in log output
+    hook_url        //  string: hook URL for notifications
+    multiqc_report  //  string: Path to MultiQC report
     trim_status        // map: pass/fail status per sample for trimming
     map_status         // map: pass/fail status per sample for mapping
     strand_status      // map: pass/fail status per sample for strandedness check
 
     main:
-
-    summary_params = paramsSummaryMap(workflow, parameters_schema: schema)
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
     trim_status
         .map{
@@ -129,7 +146,15 @@ workflow PIPELINE_COMPLETION {
     //
     workflow.onComplete {
         if (email || email_on_fail) {
-            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
+            completionEmail(
+                summary_params,
+                email,
+                email_on_fail,
+                plaintext_email,
+                outdir,
+                monochrome_logs,
+                multiqc_report.toList()
+            )
         }
 
         rnaseqSummary(monochrome_logs=monochrome_logs, pass_mapped_reads=pass_mapped_reads, pass_trimmed_reads=pass_trimmed_reads, pass_strand_check=pass_strand_check)
@@ -145,9 +170,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 //
@@ -163,7 +188,7 @@ def checkSamplesAfterGrouping(input) {
     }
 
     // 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: ${metas[0].id}")
     }
@@ -316,7 +341,6 @@ def genomeExistsError() {
         error(error_string)
     }
 }
-
 //
 // Generate methods description for MultiQC
 //
@@ -358,8 +382,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
         // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
         // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        def manifest_doi = meta.manifest_map.doi.tokenize(",")
+        manifest_doi.each { doi_ref ->
+            temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
index ea784ea01..3c1440f1a 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_completion.workflow.nf.test
@@ -9,17 +9,16 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = "${projectDir}/nextflow_schema.json" // schema (string)
-                input[1] = null // email (string)
-                input[2] = null // email_on_fail (string)
-                input[3] = true // plaintext_email (boolean)
-                input[4] = "${outputDir}" // outputDir (string)
-                input[5] = true // monochrome_logs (boolean)
-                input[6] = null // hook_url (string)
-                input[7] = "${outputDir}/multiqc_report.html" // multiqc_report (string)
+                input[0] = null // email (string)
+                input[1] = null // email_on_fail (string)
+                input[2] = true // plaintext_email (boolean)
+                input[3] = "${outputDir}" // outputDir (string)
+                input[4] = true // monochrome_logs (boolean)
+                input[5] = null // hook_url (string)
+                input[6] = "${outputDir}/multiqc_report.html" // multiqc_report (string)
+                input[7] = Channel.of(['test_sample', true])
                 input[8] = Channel.of(['test_sample', true])
                 input[9] = Channel.of(['test_sample', true])
-                input[10] = Channel.of(['test_sample', true])
                 """
             }
         }
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test
similarity index 79%
rename from subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test
rename to subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test
index c1db3fda8..87e498887 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialistion.workflow.nf.test
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/tests/main.pipeline_initialisation.workflow.nf.test
@@ -28,13 +28,11 @@ nextflow_workflow {
             }
             workflow {
                 """
-                input[0] = false                               // version (boolean)
-                input[1] = false                               // help (boolean)
-                input[2] = "${projectDir}/nextflow_schema.json" // schema (string)
-                input[3] = true                                // validate_parameters (boolean)
-                input[4] = true                                // monochrome_logs (boolean)
-                input[5] = args                                // args (array)
-                input[6] = file("$outputDir")                   // outdir (string)
+                input[0] = false                // version (boolean)
+                input[1] = true                 // validate_parameters (boolean)
+                input[2] = true                 // monochrome_logs (boolean)
+                input[3] = args                 // args (array)
+                input[4] = file("$outputDir")   // outdir (string)
                 """
             }
         }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
index b37a75c9b..264ffb222 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap
@@ -377,14 +377,14 @@
                 
             ],
             [
-                
+                null
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-07-22T17:05:49.455992"
+        "timestamp": "2024-10-09T19:19:22.192915"
     },
     "test single end read with UMI - stub": {
         "content": [
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 28e32b200..4d7f09c04 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 +90,14 @@ 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.warn("Could not verify conda channel configuration.")
+        return null
+    }
+    catch (IOException e) {
+        log.warn("Could not verify conda channel configuration.")
+        return null
     }
 
     // Check that all channels are present
@@ -106,19 +110,13 @@ def checkCondaChannels() {
 
     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]))
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
         }
     }
 
     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(
+            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\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" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        )
     }
 }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index cbd8495bb..805dcc424 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
@@ -49,12 +45,14 @@ def checkConfigProvided() {
 //
 def checkProfileProvided(nextflow_cli_args) {
     if (workflow.profile.endsWith(',')) {
-        error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
     if (nextflow_cli_args[0]) {
-        log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" +
-            "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
     }
 }
 
@@ -70,13 +68,7 @@ def workflowCitation() {
     manifest_doi.each { doi_ref ->
         temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
-        "* The pipeline\n" +
-        temp_doi_ref + "\n" +
-        "* The nf-core framework\n" +
-        "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
-        "* Software dependencies\n" +
-        "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    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 +94,7 @@ 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 +104,8 @@ def processVersionsFromYAML(yaml_file) {
 def workflowVersionToYAML() {
     return """
     Workflow:
-        $workflow.manifest.name: ${getWorkflowVersion()}
-        Nextflow: $workflow.nextflow.version
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
     """.stripIndent().trim()
 }
 
@@ -121,11 +113,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions
-                .unique()
-                .map { version -> processVersionsFromYAML(version) }
-                .unique()
-                .mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
 }
 
 //
@@ -133,25 +121,31 @@ 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
 }
@@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) {
     colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
 
     // Regular Colors
-    colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
-    colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
-    colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
-    colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
-    colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
-    colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
-    colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
-    colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
 
     // Bold
-    colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
-    colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
-    colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
-    colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
-    colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
-    colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
-    colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
-    colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
 
     // Underline
-    colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
-    colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
-    colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
-    colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
-    colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
-    colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
-    colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
-    colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
 
     // High Intensity
-    colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
-    colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
-    colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
-    colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
-    colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
-    colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
-    colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
-    colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
 
     // Bold High Intensity
-    colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
-    colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
-    colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
-    colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
-    colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
-    colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
-    colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
-    colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
 
     return colorcodes
 }
@@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) {
             mqc_report = multiqc_report.getVal()
             if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
                 if (mqc_report.size() > 1) {
-                    log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
                 }
                 mqc_report = mqc_report[0]
             }
         }
-    } catch (all) {
+    }
+    catch (Exception all) {
         if (multiqc_report) {
-            log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
         }
     }
     return mqc_report
@@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) {
 def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
 
     // Set up the e-mail variables
-    def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
     if (!workflow.success) {
-        subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
     }
 
     def summary = [:]
-    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 = [:]
@@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 
     // Render the sendmail template
     def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
-    def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
     def sendmail_html          = sendmail_template.toString()
@@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) {
+new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
-            [ 'sendmail', '-t' ].execute() << sendmail_html
-            log.info "-${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 ${email_address} (sendmail)-")
+        }
+        catch (Exception all) {
             // Catch failures and try with plaintext
-            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
-            log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
         }
     }
 
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    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 +386,14 @@ 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 +402,30 @@ 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 +450,13 @@ def imNotification(summary_params, hook_url) {
     def json_message  = json_template.toString()
 
     // POST
-    def post = new URL(hook_url).openConnection();
+    def post = new URL(hook_url).openConnection()
     post.setRequestMethod("POST")
     post.setDoOutput(true)
     post.setRequestProperty("Content-Type", "application/json")
-    post.getOutputStream().write(json_message.getBytes("UTF-8"));
-    def postRC = post.getResponseCode();
-    if (! postRC.equals(200)) {
-        log.warn(post.getErrorStream().getText());
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
     }
 }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
new file mode 100644
index 000000000..4994303ea
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -0,0 +1,46 @@
+//
+// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary
+//
+
+include { paramsSummaryLog   } from 'plugin/nf-schema'
+include { validateParameters } from 'plugin/nf-schema'
+
+workflow UTILS_NFSCHEMA_PLUGIN {
+
+    take:
+    input_workflow      // workflow: the workflow object used by nf-schema to get metadata from the workflow
+    validate_params     // boolean:  validate the parameters
+    parameters_schema   // string:   path to the parameters JSON schema.
+                        //           this has to be the same as the schema given to `validation.parametersSchema`
+                        //           when this input is empty it will automatically use the configured schema or
+                        //           "${projectDir}/nextflow_schema.json" as default. This input should not be empty
+                        //           for meta pipelines
+
+    main:
+
+    //
+    // Print parameter summary to stdout. This will display the parameters
+    // that differ from the default given in the JSON schema
+    //
+    if(parameters_schema) {
+        log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema)
+    } else {
+        log.info paramsSummaryLog(input_workflow)
+    }
+
+    //
+    // Validate the parameters using nextflow_schema.json or the schema
+    // given via the validation.parametersSchema configuration option
+    //
+    if(validate_params) {
+        if(parameters_schema) {
+            validateParameters(parameters_schema:parameters_schema)
+        } else {
+            validateParameters()
+        }
+    }
+
+    emit:
+    dummy_emit = true
+}
+
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
new file mode 100644
index 000000000..f7d9f0288
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -0,0 +1,35 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "utils_nfschema_plugin"
+description: Run nf-schema to validate parameters and create a summary of changed parameters
+keywords:
+  - validation
+  - JSON schema
+  - plugin
+  - parameters
+  - summary
+components: []
+input:
+  - input_workflow:
+      type: object
+      description: |
+        The workflow object of the used pipeline.
+        This object contains meta data used to create the params summary log
+  - validate_params:
+      type: boolean
+      description: Validate the parameters and error if invalid.
+  - parameters_schema:
+      type: string
+      description: |
+        Path to the parameters JSON schema.
+        This has to be the same as the schema given to the `validation.parametersSchema` config
+        option. When this input is empty it will automatically use the configured schema or
+        "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
+        for meta pipelines.
+output:
+  - dummy_emit:
+      type: boolean
+      description: Dummy emit to make nf-core subworkflows lint happy
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
new file mode 100644
index 000000000..842dc432a
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_workflow {
+
+    name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN"
+    script "../main.nf"
+    workflow "UTILS_NFSCHEMA_PLUGIN"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/utils_nfschema_plugin"
+    tag "plugin/nf-schema"
+
+    config "./nextflow.config"
+
+    test("Should run nothing") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = ""
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+
+    test("Should run nothing - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+            }
+
+            workflow {
+                """
+                validate_params = false
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+
+    test("Should validate params - custom schema") {
+
+        when {
+
+            params {
+                test_data   = ''
+                outdir      = 1
+            }
+
+            workflow {
+                """
+                validate_params = true
+                input[0] = workflow
+                input[1] = validate_params
+                input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
new file mode 100644
index 000000000..0907ac58f
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -0,0 +1,8 @@
+plugins {
+    id "nf-schema@2.1.0"
+}
+
+validation {
+    parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json"
+    monochromeLogs = true
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
similarity index 95%
rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 7626c1c93..331e0d2f4 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,10 +1,10 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
     "type": "object",
-    "definitions": {
+    "$defs": {
         "input_output_options": {
             "title": "Input/output options",
             "type": "object",
@@ -87,10 +87,10 @@
     },
     "allOf": [
         {
-            "$ref": "#/definitions/input_output_options"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/generic_options"
+            "$ref": "#/$defs/generic_options"
         }
     ]
 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
deleted file mode 100644
index 2585b65d1..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf
+++ /dev/null
@@ -1,62 +0,0 @@
-//
-// Subworkflow that uses the nf-validation plugin to render help text and parameter summary
-//
-
-/*
-========================================================================================
-    IMPORT NF-VALIDATION PLUGIN
-========================================================================================
-*/
-
-include { paramsHelp         } from 'plugin/nf-validation'
-include { paramsSummaryLog   } from 'plugin/nf-validation'
-include { validateParameters } from 'plugin/nf-validation'
-
-/*
-========================================================================================
-    SUBWORKFLOW DEFINITION
-========================================================================================
-*/
-
-workflow UTILS_NFVALIDATION_PLUGIN {
-
-    take:
-    print_help       // boolean: print help
-    workflow_command //  string: default commmand used to run pipeline
-    pre_help_text    //  string: string to be printed before help text and summary log
-    post_help_text   //  string: string to be printed after help text and summary log
-    validate_params  // boolean: validate parameters
-    schema_filename  //    path: JSON schema file, null to use default value
-
-    main:
-
-    log.debug "Using schema file: ${schema_filename}"
-
-    // Default values for strings
-    pre_help_text    = pre_help_text    ?: ''
-    post_help_text   = post_help_text   ?: ''
-    workflow_command = workflow_command ?: ''
-
-    //
-    // Print help message if needed
-    //
-    if (print_help) {
-        log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text
-        System.exit(0)
-    }
-
-    //
-    // Print parameter summary to stdout
-    //
-    log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text
-
-    //
-    // Validate parameters relative to the parameter JSON schema
-    //
-    if (validate_params){
-        validateParameters(parameters_schema: schema_filename)
-    }
-
-    emit:
-    dummy_emit = true
-}
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
deleted file mode 100644
index 3d4a6b04f..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "UTILS_NFVALIDATION_PLUGIN"
-description: Use nf-validation to initiate and validate a pipeline
-keywords:
-  - utility
-  - pipeline
-  - initialise
-  - validation
-components: []
-input:
-  - print_help:
-      type: boolean
-      description: |
-        Print help message and exit
-  - workflow_command:
-      type: string
-      description: |
-        The command to run the workflow e.g. "nextflow run main.nf"
-  - pre_help_text:
-      type: string
-      description: |
-        Text to print before the help message
-  - post_help_text:
-      type: string
-      description: |
-        Text to print after the help message
-  - validate_params:
-      type: boolean
-      description: |
-        Validate the parameters and error if invalid.
-  - schema_filename:
-      type: string
-      description: |
-        The filename of the schema to validate against.
-output:
-  - dummy_emit:
-      type: boolean
-      description: |
-        Dummy emit to make nf-core subworkflows lint happy
-authors:
-  - "@adamrtalbot"
-maintainers:
-  - "@adamrtalbot"
-  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
deleted file mode 100644
index 5649654e6..000000000
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ /dev/null
@@ -1,194 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
-    script "../main.nf"
-    workflow "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/tests/.nftignore b/tests/.nftignore
index dcbd8d8a8..6d2f0b8a8 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,125 +1,89 @@
-**/*DupRate_plot.{pdf,r}
-**/*Log.out
-**/*Log.{final,progress}.out
-**/*_fastqc.{html,zip}
-**/*_raw.{html,zip}
-**/*_{duprateExpBoxplot,duprateExpDens,expressionHist}.{pdf,png,svg}
-**/*bam_stat.txt
-**/*coverage.gtf
-**/*fastq.gz_trimming_report.txt
-**/*featureCounts.txt.summary
-**/*gene.abundance.txt
-**/*hisat2.summary
-**/*inner_distance*
-**/*junction*
-**/*markdup.sorted.MarkDuplicates.metrics.txt
-**/*markdup.sorted.{bam,bam.bai}
-**/*read_distribution.txt
-**/*sorted.bam.{flagstat,idxstats,stats}
-**/*sortmerna.log
-**/*splice_{events,junction}.{pdf,png,svg}
-**/*transcripts.gtf
-**/*{cnt,model,theta}
-**/*{css,gif,js}
-**/*{forward,reverse}.bigWig
-**/*{genes,isoforms}.results
-**/*{pos,seq}.DupRate.xls
-**/*{salmon,star_salmon,star_rsem}_deseq2_clustering-plot*{pdf,png,txt}
-**/Junction*.png
-**/Reads*.png
-**/abundance.{h5,tsv}
-**/cutadapt_filtered_reads_plot-{cnt,pct}.{pdf,svg}
-**/cutadapt_trimmed_sequences_*{pdf,svg}
-**/deseq2*
-**/dupradar-section-plot.{pdf,svg}
-**/fail_mapped_samples_table*
-**/fail_strand_check_table*
-**/fastqc-status-check-*{pdf,svg}
-**/fastqc_adapter_content_plot.{pdf,png,svg}
-**/fastqc_overrepresented_sequences_plot*{pdf,svg}
-**/fastqc_per_base_*_plot*{pdf,png,svg}
-**/fastqc_per_sequence_*{pdf,svg}
-**/fastqc_sequence_length_distribution_plot.{pdf,png,svg}
-**/fastqc_sequence_{counts,duplication_levels}_plot*{pdf,svg}
-**/fastqc_top_overrepresented_sequences_table*{pdf,png,svg,txt}
-**/featurecounts_biotype_plot-{cnt,pct}.{pdf,svg}
-**/fld.gz
-**/flenDist.txt
-**/general_stats_table.{pdf,png,svg}
-**/hisat2_pe_plot.txt
-**/hisat2_se_plot*{png,svg}
-**/hisat2_{pe,se}_plot-{cnt,pct}.{pdf,png,svg}
-**/junction_saturation_known.txt
-**/junction_saturation_novel.txt
-**/kallisto_alignment*{pdf,png,svg}
-**/kallisto_alignment.txt
-**/kallisto_quant.log
-**/meta_info.json
-**/multiqc_data.json
-**/multiqc_dupradar-section-plot.txt
-**/multiqc_fail_strand_check_table.txt
-**/multiqc_general_stats.txt
-**/multiqc_hisat2.txt
-**/multiqc_kallisto.txt
-**/multiqc_picard_dups.txt
-**/multiqc_plots
-**/multiqc_report.html
-**/multiqc_rsem.txt
-**/multiqc_rseqc_bam_stat.txt
-**/multiqc_rseqc_infer_experiment.txt
-**/multiqc_rseqc_junction_annotation.txt
-**/multiqc_rseqc_read_distribution.txt
-**/multiqc_salmon.txt
-**/multiqc_samtools_flagstat.txt
-**/multiqc_samtools_stats.txt
-**/multiqc_software_versions.txt
-**/multiqc_sortmerna.txt
-**/multiqc_sources.txt
-**/multiqc_star.txt
-**/multiqc_{salmon,star_salmon}_deseq2_pca-plot*txt
-**/picard_deduplication-{cnt,pct}.{pdf,png,svg}
-**/picard_deduplication.txt
-**/qualimapReport.html
-**/qualimap_gene_coverage_profile_Counts.{pdf,svg}
-**/qualimap_gene_coverage_profile_Normalised.{pdf,svg}
-**/qualimap_genomic_origin-{cnt,pct}.{pdf,png,svg}
-**/qualimap_genomic_origin.txt
-**/qualimap_rnaseq_genome_results.txt
-**/quant.genes.sf
-**/quant.sf
-**/rnaseq_qc_results.txt
-**/rsem_assignment_plot-{cnt,pct}.{pdf,png,svg}
-**/rsem_assignment_plot.txt
-**/rsem_multimapping_rates.{pdf,svg,txt}
-**/rseqc_bam_stat.{pdf,png,svg,txt}
-**/rseqc_infer_experiment_plot.{pdf,svg}
-**/rseqc_inner_*
-**/rseqc_junction_*
-**/rseqc_read_distribution_*
-**/rseqc_read_dups.txt
-**/rseqc_read_dups_plot.txt
-**/rseqc_read_dups_plot.{pdf,svg}
-**/run_info.json
-**/salmon_plot.{pdf,png,svg,txt}
-**/salmon_quant.log
-**/samtools-flagstat*
-**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Normalised_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.{pdf,svg}
-**/samtools-idxstats-mapped-reads-plot_Raw_Counts-{cnt,pct}.{pdf,svg}
-**/samtools-stats-dp.{pdf,png,svg,txt}
-**/sortmerna-detailed-plot-{cnt,pct}.{pdf,svg}
-**/sortmerna-detailed-plot.txt
-**/star_summary_table.{pdf,png,svg,txt}
-**/t_data.ctab
-**/{kallisto,salmon}.merged*
-**/{salmon,star_rsem}_deseq2_{clustering,pca}-plot.{pdf,png,svg}
-**/{salmon,star_rsem}_deseq2_{pca,pca}-plot.{pdf,png,svg}
-**/{samtools,star}_alignment_plot*
-**/{star_rsem,star_salmon}_deseq2_{clustering,pca}-plot*{pdf,png,svg}
 bbsplit/*.stats.txt
+fastqc/*/*.{html,zip}
+hisat2/log/*.hisat2.summary.log
+kallisto/*/abundance.{h5,tsv}
+kallisto/*/kallisto_quant.log
+kallisto/*/run_info.json
+kallisto/kallisto.*
 pipeline_info/*.{html,json,txt,yml}
-**/deseq2_qc/size_factors/*.txt
+sortmerna/*.sortmerna.log
+star_rsem/*.stat/*.{cnt,model,theta}
+star_rsem/*.{genes,isoforms}.results
 star_rsem/log/*.log
+star_salmon/log/*.Log.{final.out,out,progress.out}
+trimgalore/*fastq.gz_trimming_report.txt
+{hisat2,star_rsem,star_salmon}/*.{bam,bam.bai}
+{hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig
+{hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf
+{hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf
+{hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf
+{hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary
+{hisat2,star_rsem,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt
+{hisat2,star_rsem,star_salmon}/qualimap/*/css/*
+{hisat2,star_rsem,star_salmon}/qualimap/*/images_qualimapReport/*
+{hisat2,star_rsem,star_salmon}/qualimap/*/qualimapReport.html
+{hisat2,star_rsem,star_salmon}/qualimap/*/rnaseq_qc_results.txt
+{hisat2,star_rsem,star_salmon}/rseqc/bam_stat/*.bam_stat.txt
+{hisat2,star_rsem,star_salmon}/rseqc/read_distribution/*.read_distribution.txt
+{hisat2,star_rsem,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/*
+{hisat2,star_rsem,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats}
+{hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab
+{hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt
+{hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf
+{multiqc,multiqc/**}/multiqc_report.html
+{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
+{multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/hisat2_se_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
+{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
+{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc.log
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_data.json
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_hisat2.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_read_distribution.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_sortmerna.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt
+{multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt
+{multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt
+{multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt
+{multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/rsem_multimapping_rates.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_read_*.txt
+{multiqc,multiqc/**}/multiqc_report_data/salmon_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt
+{multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt
+{multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/sortmerna-detailed-plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt
+{multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt
+{multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
+{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.dds.RData
+{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.pca.vals.txt
+{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.plots.pdf
+{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt
+{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/*.txt
+{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData
+{salmon,star_salmon}/*/aux_info/fld.gz
+{salmon,star_salmon}/*/aux_info/meta_info.json
+{salmon,star_salmon}/*/libParams/flenDist.txt
+{salmon,star_salmon}/*/logs/salmon_quant.log
+{salmon,star_salmon}/*/quant.genes.sf
+{salmon,star_salmon}/*/quant.sf
+{salmon,star_salmon}/salmon.*
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 80b19646a..f47aec312 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -13,9 +13,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -24,7 +24,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -44,9 +44,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -55,7 +55,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 5bddc1cff..54f69a54b 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -83,14 +83,15 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:30:25.608093"
+        "timestamp": "2024-10-10T09:21:27.152841"
     },
     "Params: default": {
         "content": [
@@ -283,34 +284,35 @@
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt",
@@ -322,24 +324,16 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
@@ -379,32 +373,32 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -428,9 +422,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -444,40 +437,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
@@ -501,9 +492,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -517,40 +507,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
@@ -574,9 +562,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -590,8 +577,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
@@ -1301,33 +1286,33 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71",
                 "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1340,39 +1325,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6",
-                "featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304",
-                "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e",
-                "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f",
-                "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1461,103 +1413,18 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
                 "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
                 "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
-                "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
-                "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
-                "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
                 "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
                 "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
                 "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
-                "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
-                "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
-                "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
                 "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
                 "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
                 "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
-                "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
-                "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
-                "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
                 "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
                 "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
                 "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41",
-                "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3",
-                "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946",
-                "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e",
                 "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1",
                 "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
                 "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6",
-                "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5",
-                "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b",
-                "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d",
                 "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3",
                 "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b",
                 "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b",
@@ -1591,8 +1458,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.08.0"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:39:09.000328"
+        "timestamp": "2024-10-10T09:48:14.477734"
     }
 }
diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test
index fcd11c1da..daefc3fb6 100644
--- a/tests/featurecounts_group_type.nf.test
+++ b/tests/featurecounts_group_type.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
index d1f6cfb9c..5f427d903 100644
--- a/tests/featurecounts_group_type.nf.test.snap
+++ b/tests/featurecounts_group_type.nf.test.snap
@@ -83,14 +83,15 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:38:08.811967"
+        "timestamp": "2024-10-10T10:00:44.36432"
     },
     "Params: --featurecounts_group_type false": {
         "content": [
@@ -277,34 +278,35 @@
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt",
@@ -315,24 +317,16 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
@@ -372,32 +366,32 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf",
@@ -419,9 +413,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -435,40 +428,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png",
@@ -490,9 +481,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -506,40 +496,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg",
@@ -561,9 +549,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -577,8 +564,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
@@ -1267,33 +1252,33 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,b4776accd1bf7206c7ab0f1d84e4721e",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1305,37 +1290,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e",
-                "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f",
-                "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1409,103 +1363,18 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
                 "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
                 "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
-                "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
-                "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
-                "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
                 "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
                 "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
                 "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
-                "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
-                "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
-                "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
                 "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
                 "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
                 "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
-                "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
-                "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
-                "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
                 "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
                 "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
                 "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41",
-                "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3",
-                "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946",
-                "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e",
                 "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1",
                 "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211",
                 "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6",
-                "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5",
-                "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b",
-                "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d",
                 "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3",
                 "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b",
                 "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b",
@@ -1539,8 +1408,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:37:24.538529"
+        "timestamp": "2024-10-10T10:00:00.235948"
     }
 }
diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test
index e743a37d4..478205889 100644
--- a/tests/hisat2.nf.test
+++ b/tests/hisat2.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
index 8899222be..2fec710ac 100644
--- a/tests/hisat2.nf.test.snap
+++ b/tests/hisat2.nf.test.snap
@@ -84,14 +84,15 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:43:50.371605"
+        "timestamp": "2024-10-10T10:10:47.69497"
     },
     "Params: --aligner hisat2": {
         "content": [
@@ -750,36 +751,37 @@
                 "multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/hisat2/multiqc_report_data/multiqc.log",
                 "multiqc/hisat2/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_data.json",
-                "multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/hisat2/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt",
@@ -792,12 +794,8 @@
                 "multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/hisat2/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/hisat2/multiqc_report_data/multiqc_sample-relationships_1.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt",
@@ -840,32 +838,32 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -893,9 +891,8 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -912,32 +909,32 @@
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/hisat2/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/dupradar.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png",
@@ -965,9 +962,8 @@
                 "multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -984,32 +980,32 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg",
@@ -1037,9 +1033,8 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -1198,108 +1193,18 @@
                 "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794",
                 "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
                 "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c",
-                "RAP1_IAA_30M_REP1.hisat2.summary.log:md5,4273e7a9d0fa8a93ec62e25a70a7e212",
-                "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678",
-                "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9",
-                "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8",
-                "WT_REP2.hisat2.summary.log:md5,e622496abff3ce68afcd1c21a7a1e0df",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,99a8749fb819be0f1bde152e2246d964",
-                "Coverage Profile Along Genes (Low).png:md5,31bed1d299f6e763c61a2866abc847c9",
-                "Coverage Profile Along Genes (Total).png:md5,97d15c2ffd8163b800b1ca6378ae0ce9",
-                "Transcript coverage histogram.png:md5,a0cd920b7f67ee02deb4fd5ee5a5b0fc",
                 "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536",
                 "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06",
                 "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,0c9e9983e2bb5688bca25d1697bcde9c",
-                "Coverage Profile Along Genes (Low).png:md5,07df4715abe4e9c49265b7cecec79fe6",
-                "Coverage Profile Along Genes (Total).png:md5,a4ed549db9b210e43955386957fdcd49",
-                "Transcript coverage histogram.png:md5,1ee5a0ec7f0eec36dd51e312d303ea55",
                 "coverage_profile_along_genes_(high).txt:md5,9ffadadb953cc9ea1b1c01ac92fcdf61",
                 "coverage_profile_along_genes_(low).txt:md5,fb281c857a2c4e093b0d8e1f756abf81",
                 "coverage_profile_along_genes_(total).txt:md5,fb281c857a2c4e093b0d8e1f756abf81",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,9e530e83b3ab308ece285c115b7bde7d",
-                "Coverage Profile Along Genes (Low).png:md5,b4181c86e9764bf7f543b24232ffea77",
-                "Coverage Profile Along Genes (Total).png:md5,ec77f7b0919d8537f31ecf3a6dd245b0",
-                "Transcript coverage histogram.png:md5,4017dc4254884805a327a6fd45e06562",
                 "coverage_profile_along_genes_(high).txt:md5,a31cb4ba804080544072cd57fc1bdf1c",
                 "coverage_profile_along_genes_(low).txt:md5,f744e295c3d034b1a86e1dde8bb18eff",
                 "coverage_profile_along_genes_(total).txt:md5,f744e295c3d034b1a86e1dde8bb18eff",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,9e4a7aa85ae86a7ab5b1c949ed10d913",
-                "Coverage Profile Along Genes (Low).png:md5,3f9d7d3842d827bb5a7a46a80e88e14b",
-                "Coverage Profile Along Genes (Total).png:md5,44826c2d3263ff4aaedfa3b4d0c068db",
-                "Transcript coverage histogram.png:md5,51e934c908640c9dda94d3de8c4dd81f",
                 "coverage_profile_along_genes_(high).txt:md5,be72a2c9023f6eb81bd5816af33abb65",
                 "coverage_profile_along_genes_(low).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb",
                 "coverage_profile_along_genes_(total).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,f63458b8564de80c90c992926ea273ed",
-                "Coverage Profile Along Genes (Low).png:md5,44f0dd7c647a2ce2c1f06e3920266e95",
-                "Coverage Profile Along Genes (Total).png:md5,12780d9ad7b76dbdd39736099c45cf07",
-                "Transcript coverage histogram.png:md5,fcc848c9d318a28c7dff00cb2960e038",
                 "coverage_profile_along_genes_(high).txt:md5,83d436e0ddb7435bb343db5e4dfb744a",
                 "coverage_profile_along_genes_(low).txt:md5,58021e91f3595a0d6dc74abc41690638",
                 "coverage_profile_along_genes_(total).txt:md5,58021e91f3595a0d6dc74abc41690638",
@@ -1328,34 +1233,33 @@
                 "e_data.ctab:md5,22bdc84c1c4acce9798868e8c7b56004",
                 "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
                 "i_data.ctab:md5,80fe14762a8f7230d516bba37b7275d1",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
-                "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65",
                 "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1368,39 +1272,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46",
-                "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338",
-                "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d",
-                "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251",
-                "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,a56226e705754ce81c7709d40794dd92",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1437,8 +1308,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:43:07.13584"
+        "timestamp": "2024-10-10T12:37:31.888584"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test
index 0c6816a59..a964757d3 100644
--- a/tests/kallisto.nf.test
+++ b/tests/kallisto.nf.test
@@ -16,9 +16,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -50,9 +50,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -61,7 +61,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
index 4bb2324e3..a5402206e 100644
--- a/tests/kallisto.nf.test.snap
+++ b/tests/kallisto.nf.test.snap
@@ -133,18 +133,19 @@
                 "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/multiqc_report_data/kallisto_alignment.txt",
+                "multiqc/multiqc_report_data/multiqc.log",
                 "multiqc/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/multiqc_report_data/multiqc_data.json",
@@ -159,18 +160,18 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf",
                 "multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf",
@@ -179,18 +180,18 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png",
                 "multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png",
@@ -199,18 +200,18 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg",
                 "multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg",
@@ -230,41 +231,29 @@
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754"
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:46:44.393695"
+        "timestamp": "2024-10-09T19:19:07.816437"
     },
     "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
         "content": [
@@ -333,13 +322,14 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:47:31.044439"
+        "timestamp": "2024-10-09T18:56:35.320816"
     }
 }
diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test
index 7ffef71de..0572a71ac 100644
--- a/tests/min_mapped_reads.nf.test
+++ b/tests/min_mapped_reads.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
index ce656d979..2e0636eb8 100644
--- a/tests/min_mapped_reads.nf.test.snap
+++ b/tests/min_mapped_reads.nf.test.snap
@@ -190,34 +190,35 @@
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
@@ -230,24 +231,16 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
@@ -287,33 +280,33 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -337,9 +330,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -353,41 +345,39 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
@@ -411,9 +401,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -427,41 +416,39 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
@@ -485,9 +472,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -501,8 +487,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
@@ -1042,34 +1026,34 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500",
                 "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1082,39 +1066,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b",
-                "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b",
-                "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e",
-                "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42",
-                "rseqc_read_dups_plot.png:md5,bdc7281c52b54a5784aa0d714f9c255e",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1193,63 +1144,12 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
                 "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
                 "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d",
-                "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4",
-                "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a",
-                "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37",
                 "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8",
                 "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
                 "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518",
-                "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d",
-                "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50",
-                "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
                 "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3",
                 "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff",
                 "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58",
-                "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90",
-                "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8",
-                "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518",
                 "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e",
                 "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d",
                 "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d",
@@ -1273,9 +1173,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:54:27.006271"
+        "timestamp": "2024-10-10T10:36:48.24104"
     },
     "Params: --min_mapped_reads 90 - stub": {
         "content": [
@@ -1361,13 +1261,14 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T07:55:19.233936"
+        "timestamp": "2024-10-10T10:37:37.274627"
     }
 }
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 6bf8f2929..86b7ac5b4 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -14,8 +14,6 @@ params {
     // for hisat2
     hisat2_build_memory = '3.GB'
 
-    validationSchemaIgnoreParams = 'genomes,igenomes_base,modules_testdata_base_path,pipelines_testdata_base_path'
-
     // TODO: check if we rather do this or disable publishdir for all processes when testing modules/subworkflows
     outdir = 'results'
 }
@@ -31,7 +29,7 @@ process {
 
 // Impose same minimum Nextflow version as the pipeline for testing
 manifest {
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=24.04.2'
 }
 
 // Disable all Nextflow reporting options
diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test
index 66084a8c9..361c80372 100644
--- a/tests/remove_ribo_rna.nf.test
+++ b/tests/remove_ribo_rna.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
index da224c5e5..232ea90a6 100644
--- a/tests/remove_ribo_rna.nf.test.snap
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -196,34 +196,35 @@
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt",
@@ -235,12 +236,10 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt",
@@ -248,12 +247,6 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
@@ -294,32 +287,32 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -343,9 +336,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -361,40 +353,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
@@ -418,9 +408,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -436,40 +425,38 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
@@ -493,9 +480,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -511,8 +497,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
@@ -1228,33 +1212,33 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd",
                 "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1267,41 +1251,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,62ee84d3b32bdbfb9766fa970680f92c",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,ed2c5826034fcf2417afe79902897c45",
-                "featurecounts_biotype_plot-pct.png:md5,96abf028d347f568289b3a741aa8c08d",
-                "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00",
-                "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa",
-                "rseqc_read_dups_plot.png:md5,1a18ce4ca5f36722f1fdd579d7eb41e1",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,af332971e3158b3cfee3a65311ebfe2c",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,f12bcf930eac8ed45da7b4668b1169c8",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,ff8e0f61b02f8c9abcce5e83214c87fd",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a",
-                "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020",
-                "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c",
                 "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1390,103 +1339,18 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
                 "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204",
                 "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,1a837e43161d7133e9156c7b18123aa9",
-                "Coverage Profile Along Genes (Low).png:md5,46c5ba09af49602b956efd780f7a39e4",
-                "Coverage Profile Along Genes (Total).png:md5,b04cac9c2d15b1b9623d87d44caadff6",
-                "Transcript coverage histogram.png:md5,cbb250c6903bfe6ecab5fb4b2ca661e5",
                 "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba",
                 "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8",
                 "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,8c8b46f9bfb6cf952a95d85a6b917444",
-                "Coverage Profile Along Genes (Low).png:md5,5c56671f085c6db7fd86b41bb5b7e6d0",
-                "Coverage Profile Along Genes (Total).png:md5,b83fbaedfe4dcfdd7b3970d2ff27d517",
-                "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe",
                 "coverage_profile_along_genes_(high).txt:md5,f5ac8f74fcad5d9ac72dbb6b65184bd0",
                 "coverage_profile_along_genes_(low).txt:md5,d66da6e3f49b0870184fc881a162e785",
                 "coverage_profile_along_genes_(total).txt:md5,d66da6e3f49b0870184fc881a162e785",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,015aa34b0d32f38bade831a3ef497984",
-                "Coverage Profile Along Genes (Low).png:md5,5798e0d977e0fee55ec4fc5192bfc0f4",
-                "Coverage Profile Along Genes (Total).png:md5,2bbec5e165075024cb1f74a042b1385a",
-                "Transcript coverage histogram.png:md5,bfd09f8b3282958a6a73b7924edac664",
                 "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd",
                 "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3",
                 "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,d8a36870a6f262c41995b4b5bd26a149",
-                "Coverage Profile Along Genes (Low).png:md5,5570af90ee685a3c95117519aa6bdc46",
-                "Coverage Profile Along Genes (Total).png:md5,eb53e699213ce453cbea7f71f5204b08",
-                "Transcript coverage histogram.png:md5,f0bd8d82a8b7adec6e1f1ef85633eded",
                 "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb",
                 "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc",
                 "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,3c1c603d63f3f7f9ba1ab6e7749b7771",
-                "Coverage Profile Along Genes (Low).png:md5,9f80251ed043cf900fa939cc254ccc81",
-                "Coverage Profile Along Genes (Total).png:md5,a420f287f986a8db317be712ac0a2237",
-                "Transcript coverage histogram.png:md5,c467c5eac12a95f8569198927434440d",
                 "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294",
                 "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd",
                 "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd",
@@ -1520,9 +1384,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:07:16.890773"
+        "timestamp": "2024-10-10T11:03:32.596507"
     },
     "Params: --remove_ribo_rna - stub": {
         "content": [
@@ -1611,13 +1475,14 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:08:00.752563"
+        "timestamp": "2024-10-10T11:04:25.816703"
     }
 }
diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test
index c0a386da0..562b09cce 100644
--- a/tests/salmon.nf.test
+++ b/tests/salmon.nf.test
@@ -16,9 +16,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -50,9 +50,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -61,7 +61,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
index 0adf4ff4d..f09490d98 100644
--- a/tests/salmon.nf.test.snap
+++ b/tests/salmon.nf.test.snap
@@ -88,17 +88,18 @@
                 "multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_report_data/multiqc.log",
                 "multiqc/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/multiqc_report_data/multiqc_data.json",
@@ -114,18 +115,18 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/salmon_plot.pdf",
                 "multiqc/multiqc_report_plots/png",
@@ -133,18 +134,18 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/multiqc_report_plots/png/salmon_plot.png",
                 "multiqc/multiqc_report_plots/svg",
@@ -152,18 +153,18 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report_plots/svg/salmon_plot.svg",
                 "pipeline_info",
@@ -275,34 +276,22 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -338,9 +327,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:10:56.056197"
+        "timestamp": "2024-10-10T07:25:22.063836"
     },
     "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": {
         "content": [
@@ -406,13 +395,14 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:11:32.236118"
+        "timestamp": "2024-10-10T07:07:48.845197"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test
index 3c03631cc..7861f9962 100644
--- a/tests/skip_qc.nf.test
+++ b/tests/skip_qc.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
index 3d2688737..b85335408 100644
--- a/tests/skip_qc.nf.test.snap
+++ b/tests/skip_qc.nf.test.snap
@@ -69,14 +69,15 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:17:45.954114"
+        "timestamp": "2024-10-10T11:17:30.991115"
     },
     "Params: --skip_qc": {
         "content": [
@@ -208,17 +209,18 @@
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
@@ -252,18 +254,18 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf",
@@ -287,18 +289,18 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png",
@@ -322,18 +324,18 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg",
@@ -675,22 +677,22 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -698,24 +700,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -802,8 +786,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:17:03.577873"
+        "timestamp": "2024-10-10T11:16:41.081492"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test
index 5053e103f..bb4282216 100644
--- a/tests/skip_trimming.nf.test
+++ b/tests/skip_trimming.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index 715c0604b..82acf3cfd 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -166,22 +166,23 @@
                 "multiqc/star_salmon",
                 "multiqc/star_salmon/multiqc_report.html",
                 "multiqc/star_salmon/multiqc_report_data",
-                "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc.log",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt",
@@ -192,24 +193,16 @@
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt",
                 "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt",
@@ -245,20 +238,20 @@
                 "multiqc/star_salmon/multiqc_report_data/star_summary_table.txt",
                 "multiqc/star_salmon/multiqc_report_plots",
                 "multiqc/star_salmon/multiqc_report_plots/pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -282,9 +275,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -298,24 +290,22 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/png",
-                "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png",
@@ -339,9 +329,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -355,24 +344,22 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg",
@@ -396,9 +383,8 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -412,8 +398,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
@@ -1114,16 +1098,16 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
                 "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10",
@@ -1138,27 +1122,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525",
-                "dupradar-section-plot.png:md5,5e5487f0e1f1521264462d5cb9ee9089",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,dcb37b4ce2fff5ca2e22767b172e55a8",
-                "featurecounts_biotype_plot-pct.png:md5,b15370ba2c056815939251f820d9e2af",
-                "qualimap_gene_coverage_profile_Counts.png:md5,8312f777db61509caa66d1f53a4b6b07",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,66acb12427130766801a8376f95ed88b",
-                "rseqc_infer_experiment_plot.png:md5,c3108e35020ee93a77a62ea0167613b2",
-                "rseqc_read_dups_plot.png:md5,1e43ad78c4a87f7736b552ad71d25c16",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,64f2501f91db6dd0edd5e49c0b9ca8b7",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,52f30fc3448f43735ce9eca54b306c8e",
                 "ambig_info.tsv:md5,e099a9ec06de792219139248712f7f40",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1247,103 +1210,18 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3",
                 "WT_REP1.SJ.out.tab:md5,299a948b1aaf329152224ba573402a51",
                 "WT_REP2.SJ.out.tab:md5,073498a8fb5fb4da664c9129a6777c42",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,3a6e83a9a2e0e983b1191a622bfc8ef1",
-                "Coverage Profile Along Genes (Low).png:md5,1f075e71d4c281be2ecad16cf13f52bc",
-                "Coverage Profile Along Genes (Total).png:md5,f32d6ff38cfe4d01c6cbc917cb6e21c1",
-                "Transcript coverage histogram.png:md5,4e4a8d520a3018a888e5840936e9f4e0",
                 "coverage_profile_along_genes_(high).txt:md5,59a01cd5d9bc7b6096490d7f3d6d6877",
                 "coverage_profile_along_genes_(low).txt:md5,8a5255e6f9f142bbd22c636296f41d72",
                 "coverage_profile_along_genes_(total).txt:md5,8a5255e6f9f142bbd22c636296f41d72",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,a0efd6fc7c7c803a3b51e7fc4600ed98",
-                "Coverage Profile Along Genes (Low).png:md5,212d68ca87f5bc4c60ed04a33df126af",
-                "Coverage Profile Along Genes (Total).png:md5,a72b6252a3ece3fb911da724274eabae",
-                "Transcript coverage histogram.png:md5,1daabf214a2d2c32748834188c8bea5d",
                 "coverage_profile_along_genes_(high).txt:md5,61683a2fcf35174fe72a648be63d45ac",
                 "coverage_profile_along_genes_(low).txt:md5,031046ef33de379e0463fddc0b924ecd",
                 "coverage_profile_along_genes_(total).txt:md5,031046ef33de379e0463fddc0b924ecd",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,75dbf9d2b8bde265fdda486c050d5ff5",
-                "Coverage Profile Along Genes (Low).png:md5,8e792e6037158381a50e3668c54b7254",
-                "Coverage Profile Along Genes (Total).png:md5,beaf835a8aaf95df20815032a5f92622",
-                "Transcript coverage histogram.png:md5,6428ffa766e3c59ca42a9fb5e011d866",
                 "coverage_profile_along_genes_(high).txt:md5,2745780cc56258bbe587f9b6db03e9e4",
                 "coverage_profile_along_genes_(low).txt:md5,85154785601b18118ae2e6a19d0a1c0a",
                 "coverage_profile_along_genes_(total).txt:md5,85154785601b18118ae2e6a19d0a1c0a",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,6491fbf74a1444b98fdfe495b8c26a7f",
-                "Coverage Profile Along Genes (Low).png:md5,ee6b911d01b1cfbcebb5864a1f6f5fda",
-                "Coverage Profile Along Genes (Total).png:md5,f286514f978d5bcb9508a908068ff6c7",
-                "Transcript coverage histogram.png:md5,e925b300e71d23188aa45907e0754536",
                 "coverage_profile_along_genes_(high).txt:md5,6afb5ffc9ddad52f69c518e32118ac61",
                 "coverage_profile_along_genes_(low).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42",
                 "coverage_profile_along_genes_(total).txt:md5,248345fdf0f8de2a8d7d329edd0a5c42",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,f9f0caee3156d32588c12daab8895a0f",
-                "Coverage Profile Along Genes (Low).png:md5,35ac4785ed0ffb80aaeec1fb26825f4b",
-                "Coverage Profile Along Genes (Total).png:md5,781cc1b68e9f7afc30a84b7e45b06f85",
-                "Transcript coverage histogram.png:md5,a4a300dc782deea67f18e516e0c50b3b",
                 "coverage_profile_along_genes_(high).txt:md5,f7c11dace9fc4f446fc29e5db7b3ee24",
                 "coverage_profile_along_genes_(low).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d",
                 "coverage_profile_along_genes_(total).txt:md5,f53cfe3e30c560e3261818c2e6df3d5d",
@@ -1377,8 +1255,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:24:30.328195"
+        "timestamp": "2024-10-10T11:28:37.351353"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test
index 268a1fabb..8c52fb826 100644
--- a/tests/star_rsem.nf.test
+++ b/tests/star_rsem.nf.test
@@ -14,9 +14,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
@@ -46,9 +46,9 @@ nextflow_pipeline {
 
         then {
             // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null)
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +57,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    getRelativePath(stable_name, outputDir),
+                    stable_name,
                     // All files with stable contents
                     stable_path
                 ).match() }
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
index 51411c86c..cdbf5a543 100644
--- a/tests/star_rsem.nf.test.snap
+++ b/tests/star_rsem.nf.test.snap
@@ -190,34 +190,35 @@
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt",
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt",
                 "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw-status-check-heatmap.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_adapter_content_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt",
-                "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt",
                 "multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt",
                 "multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc.log",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_data.json",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt",
@@ -230,23 +231,15 @@
                 "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_1.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_2.txt",
+                "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_3.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt",
                 "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt",
-                "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt",
                 "multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt",
                 "multiqc/star_rsem/multiqc_report_data/picard_histogram.txt",
                 "multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt",
@@ -286,32 +279,32 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf",
@@ -338,9 +331,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/sample-relationships.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf",
@@ -352,39 +344,37 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/png",
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png",
@@ -411,9 +401,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/sample-relationships.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png",
@@ -425,39 +414,37 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg",
@@ -484,9 +471,8 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/sample-relationships.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg",
@@ -498,8 +484,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg",
                 "pipeline_info",
                 "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml",
                 "salmon",
@@ -1139,36 +1123,35 @@
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
                 "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28",
-                "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1",
+                "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90",
                 "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f",
                 "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
-                "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
-                "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
-                "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
-                "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
-                "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
-                "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e",
-                "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
-                "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
-                "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
-                "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
-                "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
-                "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
-                "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
-                "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c",
-                "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c",
-                "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
+                "fastqc_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b",
+                "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974",
+                "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1",
+                "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213",
+                "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420",
+                "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704",
+                "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3",
+                "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
+                "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
+                "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
+                "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
+                "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
+                "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
+                "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
+                "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
+                "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
+                "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
+                "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
-                "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804",
+                "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8",
                 "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39",
-                "multiqc_star_rsem_deseq2_pca-plot.txt:md5,7a428c83a9dec1f43ecd4fbbea664ece",
                 "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1179,40 +1162,6 @@
                 "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722",
                 "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef",
                 "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c",
-                "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2",
-                "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0",
-                "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50",
-                "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787",
-                "dupradar-section-plot.png:md5,f76a34d2eb6f2351729d79efc1434ee8",
-                "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890",
-                "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84",
-                "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f",
-                "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14",
-                "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13",
-                "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959",
-                "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16",
-                "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,eba3abf8bedb2cb20bad90c54e9c8881",
-                "fastqc_per_sequence_quality_scores_plot-1.png:md5,d2c29cae169f35744500c751b4a7366e",
-                "fastqc_per_sequence_quality_scores_plot.png:md5,42fd7369a8aca78f620164a9e887c3cb",
-                "fastqc_sequence_counts_plot-1-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8",
-                "fastqc_sequence_counts_plot-1-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0",
-                "fastqc_sequence_counts_plot-cnt.png:md5,3890d5555f2a39b46b9f6efb14cb91f2",
-                "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054",
-                "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754",
-                "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780",
-                "featurecounts_biotype_plot-cnt.png:md5,b033cedf28f1b3f6f48f1ed793160679",
-                "featurecounts_biotype_plot-pct.png:md5,1921c3931d871f8326a6a6c5c8278815",
-                "qualimap_gene_coverage_profile_Counts.png:md5,04a262d5af169d6d771e48555adab37e",
-                "qualimap_gene_coverage_profile_Normalised.png:md5,3bddc4f2a7d462996628e33daf490247",
-                "rsem_multimapping_rates.png:md5,e93d35b86e1be681eae9b6ad19e12350",
-                "rseqc_infer_experiment_plot.png:md5,1a3a792e9a6e0c0f93c082594b24e566",
-                "rseqc_read_dups_plot.png:md5,b79c01ce4697ebb7e0ebb4a3da5b44f7",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f",
-                "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,62aceda4b51ad1ae066f761de3d70d53",
-                "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,10d7c1023bcf922ac45e653a58ee13c8",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,2edc4372d981aacfceb4f16da598d63a",
-                "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,5d2286a4f77000c199ed22517338da4a",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
@@ -1271,103 +1220,18 @@
                 "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1",
                 "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
                 "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,55ed67cd9df6d42446a76f49f6e9d6c0",
-                "Coverage Profile Along Genes (Low).png:md5,cc6887aedf7b0ce65af934849ada52f7",
-                "Coverage Profile Along Genes (Total).png:md5,ebb7199f5b5c179b3d0ad66b1833d5f0",
-                "Transcript coverage histogram.png:md5,db451ddb02fa59b2e46a3b7f936dc7e4",
                 "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2",
                 "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1",
                 "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,36376d7393575a03f6e7a1c5be4f8c32",
-                "Coverage Profile Along Genes (Low).png:md5,24e1862606452bc53f928ccf086e3699",
-                "Coverage Profile Along Genes (Total).png:md5,c843e9063c3b15e4de1c0b3f680746a9",
-                "Transcript coverage histogram.png:md5,519b1b92340d1541d864e56b9a6956e0",
                 "coverage_profile_along_genes_(high).txt:md5,93822686a53dd40d3ff426ddbfc9314e",
                 "coverage_profile_along_genes_(low).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00",
                 "coverage_profile_along_genes_(total).txt:md5,bd8d58c757e4122caee4b4e8df2f4b00",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,69dfa9f3eeac16a5615a4346c1d79eab",
-                "Coverage Profile Along Genes (Low).png:md5,84776e58e5aadee6be3b6225beccd70f",
-                "Coverage Profile Along Genes (Total).png:md5,2c0ddb2c5004d2f7a65e4814281a0836",
-                "Transcript coverage histogram.png:md5,2553413f136898302067b0a289f58241",
                 "coverage_profile_along_genes_(high).txt:md5,cdb2c00c43121e3beccd7f670b34e05e",
                 "coverage_profile_along_genes_(low).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed",
                 "coverage_profile_along_genes_(total).txt:md5,1a9405c8bd7c00f3be082bfebb90b6ed",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,4a4eb6c41483181ed9d67c390868026e",
-                "Coverage Profile Along Genes (Low).png:md5,332640c6bf816ddeec23d9e12070eede",
-                "Coverage Profile Along Genes (Total).png:md5,64402bed985293e66a634199b64c98f2",
-                "Transcript coverage histogram.png:md5,72df8608131b28ee5b23bdbc8c6e4891",
                 "coverage_profile_along_genes_(high).txt:md5,70c95fbc100f14911d2cc348bdff1587",
                 "coverage_profile_along_genes_(low).txt:md5,86e56ef794277bcf1e0d121a088b8581",
                 "coverage_profile_along_genes_(total).txt:md5,86e56ef794277bcf1e0d121a088b8581",
-                "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1",
-                "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8",
-                "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64",
-                "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d",
-                "comment.png:md5,882e40f3d6a16c6ed35659b105251525",
-                "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9",
-                "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f",
-                "file.png:md5,6587e59c55e626744eb6fc11129d99a7",
-                "minus.png:md5,8d572395aa95c89584a09813ada4dfa1",
-                "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220",
-                "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b",
-                "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e",
-                "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36",
-                "Coverage Profile Along Genes (High).png:md5,8ec27bae1db26eb468ca35843e5eb557",
-                "Coverage Profile Along Genes (Low).png:md5,5bed9f6b9e27ad01f60d188f24020c6e",
-                "Coverage Profile Along Genes (Total).png:md5,bb10036285f9e01ed64048597a25766f",
-                "Transcript coverage histogram.png:md5,e36d2e717f852cc69f2658e6a901a0ec",
                 "coverage_profile_along_genes_(high).txt:md5,a73462b9ecbd1d2c45d7ca84b5f7925b",
                 "coverage_profile_along_genes_(low).txt:md5,7adc228bc15e344abb7938ea4d35a846",
                 "coverage_profile_along_genes_(total).txt:md5,7adc228bc15e344abb7938ea4d35a846",
@@ -1404,9 +1268,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:31:03.022387"
+        "timestamp": "2024-10-10T12:45:00.993602"
     },
     "Params: --aligner star_rsem - stub": {
         "content": [
@@ -1490,13 +1354,14 @@
             ],
             [
                 "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.09.0"
         },
-        "timestamp": "2024-10-02T08:31:54.433237"
+        "timestamp": "2024-10-10T11:41:09.240442"
     }
 }
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index e58d744b4..2ac6dcf86 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -49,8 +49,8 @@ include { BEDTOOLS_GENOMECOV as BEDTOOLS_GENOMECOV_REV         } from '../../mod
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
 //
-include { paramsSummaryMap                 } from 'plugin/nf-validation'
-include { fromSamplesheet                  } from 'plugin/nf-validation'
+include { paramsSummaryMap                 } from 'plugin/nf-schema'
+include { samplesheetToList                } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc             } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML           } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
 include { FASTQ_ALIGN_HISAT2               } from '../../subworkflows/nf-core/fastq_align_hisat2'
@@ -111,7 +111,7 @@ workflow RNASEQ {
     // Create channel from input file provided through params.input
     //
     Channel
-        .fromSamplesheet("input")
+        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
                 if (!fastq_2) {