diff --git a/.editorconfig b/.editorconfig
index b6b31907..9b990088 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index a0b78f39..47fda249 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -31,7 +31,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index b53e3b20..7b722e77 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: Tower debug log file
           path: |
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 7ebd2e11..6a3b05e6 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v1
+        uses: mshick/add-pr-comment@v2
         with:
           message: |
             ## This PR is against the `master` branch :x:
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 694e90ec..e37cfda5 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v7
+      - uses: actions/stale@v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
new file mode 100644
index 00000000..8611458a
--- /dev/null
+++ b/.github/workflows/download_pipeline.yml
@@ -0,0 +1,67 @@
+name: Test successful pipeline download with 'nf-core download'
+
+# Run the workflow when:
+#  - dispatched manually
+#  - when a PR is opened or reopened to master branch
+#  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
+on:
+  workflow_dispatch:
+  pull_request:
+    types:
+      - opened
+    branches:
+      - master
+  pull_request_target:
+    branches:
+      - master
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  download:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+      - uses: eWaterCycle/setup-singularity@v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install git+https://github.com/nf-core/tools.git@dev
+
+      - name: Get the repository name and current branch set as environment variable
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+
+      - name: Download the pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+        run: |
+          nf-core 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-cache-utilisation 'amend' \
+          --download-configuration
+
+      - name: Inspect download
+        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+
+      - name: Run the downloaded pipeline
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 7b5ad1c7..74c1ce02 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  fix-linting:
     # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
@@ -13,10 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -24,32 +31,59 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
 
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix code linting"
           git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/taxprofiler/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 905c58e4..81cd098e 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,61 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: 3.11
+          cache: "pip"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest
@@ -76,7 +37,7 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -99,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 0bbcd30f..147bcd10 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@v2
+        uses: dawidd6/action-download-artifact@v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 6ad33927..21ac3f06 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +56,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@v0.0.2
+      - uses: zentered/bluesky-post-action@v0.1.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.gitpod.yml b/.gitpod.yml
index acf72695..363d5b1d 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -7,6 +7,7 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0c31cdb9..af57081f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 990a8585..ccf8b640 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v1.1.3dev - [date]
+## v1.1.5dev - [date]
 
 Initial release of nf-core/taxprofiler, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index 95fe392d..225937d9 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,9 @@
-# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_dark.png#gh-dark-mode-only)
-
+<h1>
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-taxprofiler_logo_dark.png">
+    <img alt="nf-core/taxprofiler" src="docs/images/nf-core-taxprofiler_logo_light.png">
+  </picture>
+</h1>
 [![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
diff --git a/assets/email_template.html b/assets/email_template.html
index 0718cb71..c6460a26 100644
--- a/assets/email_template.html
+++ b/assets/email_template.html
@@ -12,7 +12,7 @@
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>nf-core/taxprofiler v${version}</h1>
+<h1>nf-core/taxprofiler ${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
diff --git a/assets/email_template.txt b/assets/email_template.txt
index a7d5e6bf..6ccaa334 100644
--- a/assets/email_template.txt
+++ b/assets/email_template.txt
@@ -4,7 +4,7 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/taxprofiler v${version}
+  nf-core/taxprofiler ${version}
 ----------------------------------------------------
 Run Name: $runName
 
diff --git a/assets/nf-core-taxprofiler_logo_light.png b/assets/nf-core-taxprofiler_logo_light.png
index 7e61612f..768e4904 100644
Binary files a/assets/nf-core-taxprofiler_logo_light.png and b/assets/nf-core-taxprofiler_logo_light.png differ
diff --git a/docs/images/nf-core-taxprofiler_logo_dark.png b/docs/images/nf-core-taxprofiler_logo_dark.png
index 19433254..d2134ad6 100644
Binary files a/docs/images/nf-core-taxprofiler_logo_dark.png and b/docs/images/nf-core-taxprofiler_logo_dark.png differ
diff --git a/docs/images/nf-core-taxprofiler_logo_light.png b/docs/images/nf-core-taxprofiler_logo_light.png
index 7e61612f..f5f4c4ad 100644
Binary files a/docs/images/nf-core-taxprofiler_logo_light.png and b/docs/images/nf-core-taxprofiler_logo_light.png differ
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 9a17e76a..d5f2712d 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -24,7 +24,7 @@ class WorkflowMain {
     //
     // Validate parameters and print summary to screen
     //
-    public static void initialise(workflow, params, log) {
+    public static void initialise(workflow, params, log, args) {
 
         // Print workflow version and exit on --version
         if (params.version) {
@@ -35,6 +35,8 @@ class WorkflowMain {
 
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
+        // Check that the profile doesn't contain spaces and doesn't end with a trailing comma
+        checkProfile(workflow.profile, args, log)
 
         // Check that conda channels are set-up correctly
         if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
@@ -60,4 +62,16 @@ class WorkflowMain {
         }
         return null
     }
+
+    //
+    // Exit pipeline if --profile contains spaces
+    //
+    private static void checkProfile(profile, args, log) {
+        if (profile.endsWith(',')) {
+            Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
+        }
+        if (args[0]) {
+            log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n      Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`."
+        }
+    }
 }
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
deleted file mode 100644
index 805c8bb5..00000000
Binary files a/lib/nfcore_external_java_deps.jar and /dev/null differ
diff --git a/main.nf b/main.nf
index 718fe303..635fa097 100644
--- a/main.nf
+++ b/main.nf
@@ -44,7 +44,7 @@ if (params.validate_params) {
     validateParameters()
 }
 
-WorkflowMain.initialise(workflow, params, log)
+WorkflowMain.initialise(workflow, params, log, args)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/modules.json b/modules.json
index eef119e2..1303902b 100644
--- a/modules.json
+++ b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
+                        "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
index f0c63f69..9b3272bc 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.17
+  - bioconda::multiqc=1.19
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 7685b33c..f2187611 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.17--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
index eec1db10..b1e1630b 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -31,7 +31,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.mqc_yml[0]).readLines()[0..10],
+                    file(process.out.yml[0]).readLines()[0..7]
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
index 4274ed57..5f59a936 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -1,27 +1,33 @@
 {
     "Should run without failures": {
         "content": [
-            {
-                "0": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ],
-                "1": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "2": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "mqc_yml": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "versions": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "yml": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ]
-            }
+            [
+                "versions.yml:md5,76d454d92244589d32455833f7c1ba6d"
+            ],
+            [
+                "data: \"<style>\\n#nf-core-versions tbody:nth-child(even) {\\n    background-color: #f2f2f2;\\n\\",
+                "  }\\n</style>\\n<table class=\\\"table\\\" style=\\\"width:100%\\\" id=\\\"nf-core-versions\\\"\\",
+                "  >\\n    <thead>\\n        <tr>\\n            <th> Process Name </th>\\n            <th>\\",
+                "  \\ Software </th>\\n            <th> Version  </th>\\n        </tr>\\n    </thead>\\n\\",
+                "  \\n<tbody>\\n<tr>\\n    <td><samp>CUSTOM_DUMPSOFTWAREVERSIONS</samp></td>\\n    <td><samp>python</samp></td>\\n\\",
+                "  \\    <td><samp>3.11.7</samp></td>\\n</tr>\\n\\n<tr>\\n    <td><samp></samp></td>\\n \\",
+                "  \\   <td><samp>yaml</samp></td>\\n    <td><samp>5.4.1</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>TOOL1</samp></td>\\n    <td><samp>tool1</samp></td>\\n\\",
+                "  \\    <td><samp>0.11.9</samp></td>\\n</tr>\\n\\n</tbody>\\n<tbody>\\n<tr>\\n    <td><samp>TOOL2</samp></td>\\n\\",
+                "  \\    <td><samp>tool2</samp></td>\\n    <td><samp>1.9</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>Workflow</samp></td>\\n    <td><samp>Nextflow</samp></td>\\n\\"
+            ],
+            [
+                "CUSTOM_DUMPSOFTWAREVERSIONS:",
+                "  python: 3.11.7",
+                "  yaml: 5.4.1",
+                "TOOL1:",
+                "  tool1: 0.11.9",
+                "TOOL2:",
+                "  tool2: '1.9'",
+                "Workflow:"
+            ]
         ],
-        "timestamp": "2023-11-03T14:43:22.157011"
+        "timestamp": "2024-01-09T23:01:18.710682"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
index b9e8f926..1f21c664 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -3,24 +3,20 @@ nextflow_process {
     name "Test Process FASTQC"
     script "../main.nf"
     process "FASTQC"
+
     tag "modules"
     tag "modules_nfcore"
     tag "fastqc"
 
-    test("Single-Read") {
+    test("sarscov2 single-end [fastq]") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id: 'test', single_end:true ],
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 """
             }
         }
@@ -28,82 +24,189 @@ nextflow_process {
         then {
             assertAll (
             { assert process.success },
+
             // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
             // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
             // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
-            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert snapshot(process.out.versions).match("versions") },
-            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
             )
         }
     }
-// TODO
-// //
-// // Test with paired-end data
-// //
-// workflow test_fastqc_paired_end {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 [
-//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-//                 ]
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with interleaved data
-// //
-// workflow test_fastqc_interleaved {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with bam data
-// //
-// workflow test_fastqc_bam {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with multiple samples
-// //
-// workflow test_fastqc_multiple {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 [
-//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
-//                 ]
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with custom prefix
-// //
-// workflow test_fastqc_custom_prefix {
-//     input = [
-//                 [ id:'mysample', single_end:true ], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
+                                process.out.zip.collect { file(it[1]).getName() } +
+                                process.out.versions ).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
index 636a32ce..5d624bb8 100644
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,10 +1,20 @@
 {
+    "sarscov2 single-end [fastq] - stub": {
+        "content": [
+            [
+                "test.html",
+                "test.zip",
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "timestamp": "2024-01-17T18:40:57.254299"
+    },
     "versions": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2023-10-09T23:40:54+0000"
+        "timestamp": "2024-01-17T18:36:50.033627"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index bc0bdb5b..7625b752 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=1.18
+  - bioconda::multiqc=1.19
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 00cc48d2..1b9f7c43 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:1.18--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.18--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -43,7 +43,7 @@ process MULTIQC {
 
     stub:
     """
-    touch multiqc_data
+    mkdir multiqc_data
     touch multiqc_plots
     touch multiqc_report.html
 
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index f1aa660e..45a9bc35 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: multiqc
 description: Aggregate results from bioinformatics analyses across many samples into a single report
 keywords:
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index c2dad217..d0438eda 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -7,12 +7,9 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
-    test("MULTIQC: FASTQC") {
+    test("sarscov2 single-end [fastqc]") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             process {
                 """
                 input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
@@ -26,20 +23,17 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.report.get(0)).exists() },
-                { assert path(process.out.data.get(0)).exists() },
-                { assert path(process.out.versions.get(0)).getText().contains("multiqc") }
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("versions") }
             )
         }
 
     }
 
-    test("MULTIQC: FASTQC and a config file") {
+    test("sarscov2 single-end [fastqc] [config]") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             process {
                 """
                 input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
@@ -53,9 +47,35 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.report.get(0)).exists() },
-                { assert path(process.out.data.get(0)).exists() },
-                { assert path(process.out.versions.get(0)).getText().contains("multiqc") }
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.report.collect { file(it).getName() } +
+                                process.out.data.collect { file(it).getName() } +
+                                process.out.plots.collect { file(it).getName() } +
+                                process.out.versions ).match() }
             )
         }
 
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
new file mode 100644
index 00000000..d37e7304
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
+            ]
+        ],
+        "timestamp": "2024-01-09T23:02:49.911994"
+    },
+    "sarscov2 single-end [fastqc] - stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
+            ]
+        ],
+        "timestamp": "2024-01-09T23:03:14.524346"
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 4c07236a..bd2bd8c6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -71,7 +71,7 @@ try {
 }
 
 // Load nf-core/taxprofiler custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
 // try {
 //   includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
 // } catch (Exception e) {
@@ -91,6 +91,7 @@ profiles {
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        channels               = ['conda-forge', 'bioconda', 'defaults']
         apptainer.enabled      = false
     }
     mamba {
@@ -233,7 +234,7 @@ manifest {
     description     = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.3dev'
+    version         = '1.1.5dev'
     doi             = ''
 }
 
diff --git a/pyproject.toml b/pyproject.toml
index 0d62beb6..7d08e1c8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,10 +1,13 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# 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.black]
+[tool.ruff]
 line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
+target-version = "py38"
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+cache-dir = "~/.cache/ruff"
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index b3836b40..0a3061b2 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -127,6 +127,13 @@ workflow.onComplete {
     }
 }
 
+workflow.onError {
+    if (workflow.errorReport.contains("Process requirement exceeds available memory")) {
+        println("🛑 Default resources exceed availability 🛑 ")
+        println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡")
+    }
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END