diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 4ecfbfe..b290e09 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -10,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.
diff --git a/.editorconfig b/.editorconfig
index dd9ffa5..72dda28 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 98cc2fc..ab58b3b 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/epitopeprediction then the best place to ask is on the nf-core Slack [#epitopeprediction](https://nfcore.slack.com/channels/epitopeprediction) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 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.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+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.
 
 ### Naming schemes
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 6fc0856..47c835e 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -8,13 +8,13 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/epitopeprediction'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
+      - name: Launch workflow via Seqera Platform
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -28,9 +28,9 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 6e4dc60..91beaea 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -5,14 +5,14 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/epitopeprediction'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,9 +25,9 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6859253..afa0e35 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -28,10 +28,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index f823210..2d20d64 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           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: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 5b20cfe..91f4948 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 748b431..1fcafe8 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875..40acc23 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index c3674af..03ecfcf 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ 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' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.gitpod.yml b/.gitpod.yml
index 363d5b1..105a182 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -10,13 +10,11 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - 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 8b4d3e7..4ed619c 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -4,3 +4,4 @@ lint:
     - assets/nf-core-epitopeprediction_logo_light.png
     - docs/images/nf-core-epitopeprediction_logo_light.png
     - docs/images/nf-core-epitopeprediction_logo_dark.png
+nf_core_version: "2.14.1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af57081..4dc0f1d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e33d11..5c3762e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.3.1 - Oesterberg - 2024-05-17
+
+### `Changed`
+
+- [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Update to nf-core template `2.14.1`
+- [#237](https://github.com/nf-core/epitopeprediction/pull/237) - Update to nf-core template `2.13.1`
+
+### `Fixed`
+
+- [#243](https://github.com/nf-core/epitopeprediction/pull/243) - Add check for protein map to prevent failure if no information is available
+
 ## v2.3.0 - Oesterberg - 2024-02-26
 
 ### `Changed`
diff --git a/README.md b/README.md
index 8fe7ad9..0b80087 100644
--- a/README.md
+++ b/README.md
@@ -5,14 +5,15 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/epitopeprediction/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
+[![GitHub Actions CI Status](https://github.com/nf-core/epitopeprediction/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/epitopeprediction/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/epitopeprediction/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/epitopeprediction/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
+[![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/)
 [![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/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7?labelColor=000000)](https://tower.nf/launch?pipeline=https://github.com/nf-core/epitopeprediction)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/epitopeprediction)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23epitopeprediction-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/epitopeprediction)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 00ebcf7..5f09ac4 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/releases/tag/2.3.0" target="_blank">nf-core/epitopeprediction</a>
+  This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/releases/tag/2.3.1" target="_blank">nf-core/epitopeprediction</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/epitopeprediction/2.3.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/epitopeprediction/2.3.1/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-epitopeprediction-methods-description":
diff --git a/bin/epaa.py b/bin/epaa.py
index 65a3151..cd838ae 100755
--- a/bin/epaa.py
+++ b/bin/epaa.py
@@ -425,6 +425,11 @@ def read_lig_ID_values(filename):
 
 def create_protein_column_value(pep):
     # retrieve Ensembl protein ID for given transcript IDs, if we want to provide additional protein ID types, adapt here
+    # we have to catch cases where no protein information is available, e.g. if there are issues on BioMart side
+    if transcriptProteinTable is None:
+        logger.warning(f"Protein mapping not available for peptide {str(pep)}")
+        return ""
+
     all_proteins = [
         # split by : otherwise epytope generator suffix included
         transcriptProteinTable.query(f'transcript_id == "{transcript.transcript_id.split(":")[0]}"')["ensembl_id"]
diff --git a/conf/base.config b/conf/base.config
index 80b52ab..788deae 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -53,7 +53,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 6ee473f..c862df6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -20,14 +20,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/conf/test.config b/conf/test.config
index 749c8e3..c9181af 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -16,7 +16,7 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
diff --git a/conf/test_full.config b/conf/test_full.config
index b21c2b3..0ed2aa9 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -15,6 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_full_test.csv'
+    input = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_full_test.csv'
     tools = 'syfpeithi,mhcflurry,mhcnuggets-class-1,mhcnuggets-class-2'
+
 }
diff --git a/conf/test_grch38.config b/conf/test_grch38.config
index 0c2bbd0..4740d3c 100644
--- a/conf/test_grch38.config
+++ b/conf/test_grch38.config
@@ -13,6 +13,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     genome_reference = 'grch38'
 }
diff --git a/conf/test_mhcflurry.config b/conf/test_mhcflurry.config
index 7558693..3cab934 100644
--- a/conf/test_mhcflurry.config
+++ b/conf/test_mhcflurry.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants.csv'
     tools = 'mhcflurry'
 }
diff --git a/conf/test_mhcnuggets.config b/conf/test_mhcnuggets.config
index 90774b5..bd51993 100644
--- a/conf/test_mhcnuggets.config
+++ b/conf/test_mhcnuggets.config
@@ -16,6 +16,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_variants_class1_and_2.csv'
     tools = 'mhcnuggets-class-1,mhcnuggets-class-2'
 }
diff --git a/conf/test_netmhc.config b/conf/test_netmhc.config
index 1ad878a..56cf70f 100644
--- a/conf/test_netmhc.config
+++ b/conf/test_netmhc.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhc-4.0'
     netmhc_path = './non-free/netmhc.tar.gz'
diff --git a/conf/test_netmhcii.config b/conf/test_netmhcii.config
index 2cc2804..1b58fb1 100644
--- a/conf/test_netmhcii.config
+++ b/conf/test_netmhcii.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhcii-2.2'
     netmhcii_path = './non-free/netmhcii.tar.Z'
diff --git a/conf/test_netmhciipan.config b/conf/test_netmhciipan.config
index 07b2781..30e3a7d 100644
--- a/conf/test_netmhciipan.config
+++ b/conf/test_netmhciipan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_class2.csv'
 
     tools = 'netmhciipan-4.1'
     netmhciipan_path = './non-free/netmhciipan.tar.gz'
diff --git a/conf/test_netmhcpan.config b/conf/test_netmhcpan.config
index 2e9fb4f..b1bc950 100644
--- a/conf/test_netmhcpan.config
+++ b/conf/test_netmhcpan.config
@@ -16,7 +16,7 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 
     tools = 'netmhcpan-4.0'
     netmhcpan_path = './non-free/netmhcpan.tar.gz'
diff --git a/conf/test_peptides.config b/conf/test_peptides.config
index 74c98f3..499b31d 100644
--- a/conf/test_peptides.config
+++ b/conf/test_peptides.config
@@ -13,5 +13,5 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
 }
diff --git a/conf/test_peptides_h2.config b/conf/test_peptides_h2.config
index 26a4e00..21582dd 100644
--- a/conf/test_peptides_h2.config
+++ b/conf/test_peptides_h2.config
@@ -13,6 +13,6 @@ params {
     max_time = 48.h
 
     // Input data
-    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_mouse.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides_mouse.csv'
     tools = 'mhcnuggets-class-1'
 }
diff --git a/conf/test_proteins.config b/conf/test_proteins.config
index 7515999..084c75b 100644
--- a/conf/test_proteins.config
+++ b/conf/test_proteins.config
@@ -13,5 +13,5 @@ params {
     max_time = 4.h
 
     // Input data
-    input = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/sample_sheets/sample_sheet_proteins.csv'
+    input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_proteins.csv'
 }
diff --git a/docs/usage.md b/docs/usage.md
index 08ff5e3..177b2fc 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -200,6 +200,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index 33101bb..1934280 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
-                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
@@ -17,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
+                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     }
                 }
@@ -26,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/local/cat_files.nf b/modules/local/cat_files.nf
index 20ca1e2..1e9bce0 100644
--- a/modules/local/cat_files.nf
+++ b/modules/local/cat_files.nf
@@ -30,4 +30,19 @@ process CAT_FILES {
         cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*BusyBox //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def fileExt = input[0].name.tokenize("\\.")[-1]
+    def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}"
+    def type = fileExt == "tsv" ? "prediction_result" : "prediction_proteins"
+
+    """
+    touch ${prefix}_${type}.${fileExt}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*BusyBox //; s/ .*\$//')
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/local/csvtk_concat.nf b/modules/local/csvtk_concat.nf
index 31a0005..f3d986c 100644
--- a/modules/local/csvtk_concat.nf
+++ b/modules/local/csvtk_concat.nf
@@ -26,4 +26,14 @@ process CSVTK_CONCAT {
         csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${meta.sample}_prediction_result.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/epytope_check_requested_models.nf b/modules/local/epytope_check_requested_models.nf
index 8438c4d..2c189a4 100644
--- a/modules/local/epytope_check_requested_models.nf
+++ b/modules/local/epytope_check_requested_models.nf
@@ -47,4 +47,17 @@ process EPYTOPE_CHECK_REQUESTED_MODELS {
         epytope: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)"))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch model_report.txt
+    touch model_warnings.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mhcflurry: \$(echo \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//') )
+        mhcnuggets: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)"))
+        epytope: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)"))
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/epytope_generate_peptides.nf b/modules/local/epytope_generate_peptides.nf
index d79ce4a..20bba5e 100644
--- a/modules/local/epytope_generate_peptides.nf
+++ b/modules/local/epytope_generate_peptides.nf
@@ -35,4 +35,16 @@ process EPYTOPE_GENERATE_PEPTIDES {
         python: \$(python --version 2>&1 | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}_peptides"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        epytope: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)")
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/epytope_peptide_prediction.nf b/modules/local/epytope_peptide_prediction.nf
index ef0c07a..a001dd5 100644
--- a/modules/local/epytope_peptide_prediction.nf
+++ b/modules/local/epytope_peptide_prediction.nf
@@ -44,9 +44,10 @@ process EPYTOPE_PEPTIDE_PREDICTION {
 
     def netmhc_paths_string = netmhc_paths.join(",")
     def tools_split = params.tools.split(',')
+    // TODO: Move to nf-validation
     def class1_tools = tools_split.findAll { ! it.matches('.*(?i)(class-2|ii).*') }
     def class2_tools = tools_split.findAll { it.matches('.*(?i)(syf|class-2|ii).*') }
-
+    // TODO: Move to nf-validation
     if (((meta.mhc_class == "I") & class1_tools.empty) | ((meta.mhc_class == "II") & class2_tools.empty)) {
         exit 1, "No tools specified for mhc class ${meta.mhc_class}"
     }
@@ -88,4 +89,21 @@ process EPYTOPE_PEPTIDE_PREDICTION {
         mhcnuggets: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)")
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${splitted.baseName}.json
+    touch ${splitted.baseName}.tsv
+    touch ${splitted.baseName}.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+        epytope: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)")
+        pandas: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)")
+        pyvcf: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('PyVCF3').version)")
+        mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
+        mhcnuggets: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)")
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/external_tools_import.nf b/modules/local/external_tools_import.nf
index ccf299e..70e44e2 100644
--- a/modules/local/external_tools_import.nf
+++ b/modules/local/external_tools_import.nf
@@ -83,4 +83,14 @@ process EXTERNAL_TOOLS_IMPORT {
         ${toolname}: ${toolversion}
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir "${toolname}"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ${toolname}: ${toolversion}
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/get_prediction_versions.nf b/modules/local/get_prediction_versions.nf
index 939221b..2bc571a 100644
--- a/modules/local/get_prediction_versions.nf
+++ b/modules/local/get_prediction_versions.nf
@@ -32,6 +32,17 @@ process GET_PREDICTION_VERSIONS {
         done
     fi
     """
+
+    stub:
+    """
+    touch versions.csv
+
+    cat <<-END_VERSIONS > versions.csv
+    mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
+    mhcnuggets: \$(python -c "import pkg_resources; print('mhcnuggets' + pkg_resources.get_distribution('mhcnuggets').version)" | sed 's/^mhcnuggets//; s/ .*\$//' )
+    epytope: \$(python -c "import pkg_resources; print('epytope' + pkg_resources.get_distribution('epytope').version)" | sed 's/^epytope//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
 
 
diff --git a/modules/local/merge_json.nf b/modules/local/merge_json.nf
index 5d66f78..953f2d5 100644
--- a/modules/local/merge_json.nf
+++ b/modules/local/merge_json.nf
@@ -29,4 +29,14 @@ process MERGE_JSON {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${meta.sample}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/snpsift_split.nf b/modules/local/snpsift_split.nf
index 1e7f218..c4a8b25 100644
--- a/modules/local/snpsift_split.nf
+++ b/modules/local/snpsift_split.nf
@@ -25,4 +25,15 @@ process SNPSIFT_SPLIT {
         snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${input_file.baseName}.chr1.vcf
+    touch ${input_file.baseName}.chr2.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/split_peptides.nf b/modules/local/split_peptides.nf
index 3ade5b8..998b18a 100644
--- a/modules/local/split_peptides.nf
+++ b/modules/local/split_peptides.nf
@@ -29,4 +29,16 @@ process SPLIT_PEPTIDES {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.suffix ? "${peptide.baseName}_${task.ext.suffix}" : "${peptide.baseName}"
+    """
+    touch ${prefix}_1.tsv
+    touch ${prefix}_2.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/variant_split.nf b/modules/local/variant_split.nf
index e0695c3..f66b4c5 100644
--- a/modules/local/variant_split.nf
+++ b/modules/local/variant_split.nf
@@ -29,4 +29,14 @@ process VARIANT_SPLIT {
     END_VERSIONS
     """
 
+    stub:
+    """
+    touch ${input_file.baseName}_1.vcf
+    touch ${input_file.baseName}_2.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 2212096..ca39fb6 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.20
+  - bioconda::multiqc=1.21
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 354f443..47ac352 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:1.20--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.20--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index c204b48..bfebd80 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,d320d4c37e349c5588e07e7a31cd4186"
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-14T09:28:51.744211298"
+        "timestamp": "2024-02-29T08:48:55.657331"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186"
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-14T09:29:28.847433492"
+        "timestamp": "2024-02-29T08:49:49.071937"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186"
+                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-14T09:29:13.223621555"
+        "timestamp": "2024-02-29T08:49:25.457567"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 8308702..769a7e1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -18,6 +18,7 @@ params {
 
     // References
     genome_reference = 'grch37'
+    igenomes_ignore  = true
 
     // Options: Predictions
     tools                   = 'syfpeithi'
@@ -66,9 +67,7 @@ params {
     hook_url                   = null
     help                       = false
     version                    = false
-    validate_params            = true
-    show_hidden_params         = false
-    igenomes_ignore            = true
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
 
     // Config options
     config_profile_name        = null
@@ -104,103 +103,109 @@ try {
 }
 
 // Load nf-core/epitopeprediction custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/epitopeprediction.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/epitopeprediction profiles: ${params.custom_config_base}/pipeline/epitopeprediction.config")
-// }
+try {
+    includeConfig "${params.custom_config_base}/pipeline/epitopeprediction.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/epitopeprediction profiles: ${params.custom_config_base}/pipeline/epitopeprediction.config")
+}
 profiles {
     debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
+        dumpHashes              = true
+        process.beforeScript    = 'echo $HOSTNAME'
+        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        channels               = ['conda-forge', 'bioconda', 'defaults']
-        apptainer.enabled      = false
+        conda.enabled           = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        apptainer.enabled       = false
     }
     mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        conda.useMamba          = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     docker {
-        docker.enabled         = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+    }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
     }
     gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
     }
     test { includeConfig 'conf/test.config' }
     test_grch38 { includeConfig 'conf/test_grch38.config' }
@@ -279,7 +284,7 @@ manifest {
     description     = """A fully reproducible and state of the art epitope prediction pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.3.0'
+    version         = '2.3.1'
     doi             = ''
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 90ec20f..b3b981a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -416,12 +416,12 @@
                     "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)."
                 },
-                "show_hidden_params": {
-                    "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."
+                "pipelines_testdata_base_path": {
+                    "type": "string",
+                    "fa_icon": "far fa-check-circle",
+                    "description": "Base URL or local path to location of pipeline test dataset files",
+                    "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
+                    "hidden": true
                 }
             }
         }
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 5611062..0000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
-# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.ruff]
-line-length = 120
-target-version = "py38"
-cache-dir = "~/.cache/ruff"
-
-[tool.ruff.lint]
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
-
-[tool.ruff.lint.isort]
-known-first-party = ["nf_core"]
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
diff --git a/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf b/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf
index e62cbd1..b07d54d 100644
--- a/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_epitopeprediction_pipeline/main.nf
@@ -1,5 +1,5 @@
 //
-// Subworkflow with functionality specific to the nf-core/pipeline pipeline
+// Subworkflow with functionality specific to the nf-core/epitopeprediction pipeline
 //
 
 /*
@@ -124,6 +124,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
@@ -136,7 +140,9 @@ workflow PIPELINE_COMPLETION {
 //
 def validateInputParameters() {
     genomeExistsError()
-}//
+}
+
+//
 // Validate channels from input samplesheet
 //
 def validateInputSamplesheet(input) {
@@ -174,7 +180,9 @@ def genomeExistsError() {
             "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         error(error_string)
     }
-}//
+}
+
+//
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
@@ -216,8 +224,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["manifest_map"] = workflow.manifest.toMap()
 
     // Pipeline DOI
-    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-    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>"
+    if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
+        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>), "
+        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>"
 
     meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
     meta["tool_bibliography"] = toolBibliographyText()
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
index 8ed4310..68718e4 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -51,4 +51,4 @@ nextflow_function {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
index db2030f..e3f0baf 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap
@@ -3,10 +3,18 @@
         "content": [
             "v9.9.9"
         ],
-        "timestamp": "2024-01-19T11:32:36.031083"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:05.308243"
     },
     "Test Function checkCondaChannels": {
         "content": null,
-        "timestamp": "2024-01-19T11:32:50.456"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:12.425833"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index f7c54bc..ca964ce 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -11,9 +11,6 @@ nextflow_workflow {
     test("Should run no inputs") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 print_version        = false
@@ -39,9 +36,6 @@ nextflow_workflow {
     test("Should print version") {
 
         when {
-            params {
-                outdir = "tests/results"
-            }
             workflow {
                 """
                 print_version        = true
@@ -68,19 +62,16 @@ nextflow_workflow {
     test("Should dump params") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             workflow {
                 """
                 print_version        = false
                 dump_parameters      = true
-                outdir               = params.outdir
+                outdir               = 'results'
                 check_conda_channels = false
 
                 input[0] = false
                 input[1] = true
-                input[2] = params.outdir
+                input[2] = outdir
                 input[3] = false
                 """
             }
@@ -96,19 +87,16 @@ nextflow_workflow {
     test("Should not create params JSON if no output directory") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             workflow {
                 """
                 print_version        = false
                 dump_parameters      = true
-                outdir               = params.outdir
+                outdir               = null
                 check_conda_channels = false
 
                 input[0] = false
                 input[1] = true
-                input[2] = null
+                input[2] = outdir
                 input[3] = false
                 """
             }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index 53574ff..d0a926b 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -6,4 +6,4 @@ manifest {
     nextflowVersion  = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
-}
\ No newline at end of file
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6..14558c3 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 10f948e..1037232 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,25 +1,41 @@
 {
     "Test Function checkProfileProvided": {
         "content": null,
-        "timestamp": "2024-02-09T15:43:55.145717"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
     },
     "Test Function checkConfigProvided": {
         "content": [
             true
         ],
-        "timestamp": "2024-01-19T11:34:13.548431224"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:59.729647"
     },
     "Test Function nfCoreLogo": {
         "content": [
             "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
         ],
-        "timestamp": "2024-01-19T11:34:38.840454873"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:10.562934"
     },
     "Test Function workflowCitation": {
         "content": [
             "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
         ],
-        "timestamp": "2024-01-19T11:34:22.24352016"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:07.019761"
     },
     "Test Function without logColours": {
         "content": [
@@ -73,13 +89,21 @@
                 "biwhite": ""
             }
         ],
-        "timestamp": "2024-01-19T11:35:04.418416984"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:17.969323"
     },
     "Test Function dashedLine": {
         "content": [
             "-\u001b[2m----------------------------------------------------\u001b[0m-"
         ],
-        "timestamp": "2024-01-19T11:34:55.420000755"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:14.366181"
     },
     "Test Function with logColours": {
         "content": [
@@ -133,6 +157,10 @@
                 "biwhite": "\u001b[1;97m"
             }
         ],
-        "timestamp": "2024-01-19T11:35:13.436366565"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
index d07ce54..859d103 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -10,6 +10,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-19T11:35:22.538940073"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index 517ee54..5784a33 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -197,4 +197,4 @@ nextflow_workflow {
             )
         }
     }
-}
\ No newline at end of file
+}
diff --git a/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf
index a1060bf..4f38b8d 100644
--- a/workflows/epitopeprediction.nf
+++ b/workflows/epitopeprediction.nf
@@ -119,7 +119,7 @@ workflow EPITOPEPREDICTION {
             protein : filename.endsWith('.fasta') || filename.endsWith('.fa')
                 return [[sample:sample.id, alleles:allele_list, mhc_class:mhc_class, inputtype:'protein'], filename ]}
         .set { ch_samplesheet }
-    ch_samplesheet.peptide.view()
+
     // gunzip variant files
     GUNZIP_VCF (
         ch_samplesheet.variant_compressed
@@ -415,22 +415,44 @@ workflow EPITOPEPREDICTION {
     // Collate and save software versions
     //
     softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
-        .set { ch_collated_versions }
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_pipeline_software_mqc_versions.yml',
+            sort: true,
+            newLine: true
+        ).set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+    ch_multiqc_config        = Channel.fromPath(
+        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ?
+        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        Channel.empty()
+    ch_multiqc_logo          = params.multiqc_logo ?
+        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        Channel.empty()
+
+    summary_params      = paramsSummaryMap(
+        workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
+        file(params.multiqc_methods_description, checkIfExists: true) :
+        file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description                = Channel.value(
+        methodsDescriptionText(ch_multiqc_custom_methods_description))
+
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files = ch_multiqc_files.mix(
+        ch_methods_description.collectFile(
+            name: 'methods_description_mqc.yaml',
+            sort: true
+        )
+    )
 
     MULTIQC (
         ch_multiqc_files.collect(),