From 637b4858260d77871c3e5469659d8d3bed90f6bb Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 12 Dec 2024 11:23:53 +0000
Subject: [PATCH 1/8] Template update for nf-core/tools version 3.1.0

---
 .github/CONTRIBUTING.md                       |  12 +-
 .github/workflows/awsfulltest.yml             |  21 +-
 .github/workflows/branch.yml                  |  18 +-
 .github/workflows/ci.yml                      |   2 +-
 .github/workflows/download_pipeline.yml       |   8 +-
 .github/workflows/fix-linting.yml             |   4 +-
 .github/workflows/linting.yml                 |  10 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/release-announcements.yml   |   2 +-
 .../workflows/template_version_comment.yml    |   2 +-
 .gitpod.yml                                   |  11 +-
 .nf-core.yml                                  |   6 +-
 .vscode/settings.json                         |   3 +
 conf/base.config                              |   2 +-
 conf/modules.config                           |   1 +
 docs/usage.md                                 |  32 +-
 modules.json                                  |   8 +-
 modules/nf-core/fastqc/main.nf                |   2 +-
 modules/nf-core/fastqc/meta.yml               |   1 +
 nextflow.config                               |  77 ++++-
 nextflow_schema.json                          |   6 +
 ro-crate-metadata.json                        | 324 ++++++++++++++++++
 .../utils_nfcore_funcscan_pipeline/main.nf    |   7 +-
 .../nf-core/utils_nextflow_pipeline/main.nf   |   2 +
 .../tests/main.workflow.nf.test               |  10 +-
 .../nf-core/utils_nfcore_pipeline/main.nf     |  89 ++---
 .../tests/main.function.nf.test               |  46 +--
 .../tests/main.function.nf.test.snap          |  30 --
 .../utils_nfschema_plugin/tests/main.nf.test  |   4 +-
 workflows/funcscan.nf                         |   2 +-
 30 files changed, 526 insertions(+), 218 deletions(-)
 create mode 100644 .vscode/settings.json
 create mode 100644 ro-crate-metadata.json

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 8f39e21b..a5434a32 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# nf-core/funcscan: Contributing Guidelines
+# `nf-core/funcscan`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving nf-core/funcscan.
@@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 ## Getting help
 
@@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/funcscan documentation
 
 ## Pipeline contribution conventions
 
-To make the nf-core/funcscan code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/funcscan` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index cb53debf..47953c77 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -1,11 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:
@@ -18,18 +19,30 @@ jobs:
     if: github.repository == 'nf-core/funcscan' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - uses: octokit/request-action@v2.x
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
           CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 6e4495ad..4815e1eb 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/funcscan'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e6930d68..72e51e1f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -45,7 +45,7 @@ jobs:
             profile: "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 713dc3e7..2576cc0c 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,9 +17,11 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:
@@ -35,7 +37,7 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -69,7 +71,7 @@ jobs:
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \
+          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index f0aa68f2..5a7d4983 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index a502573c..dbd52d5a 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,12 +31,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
@@ -74,7 +74,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 42e519bf..0bed96d3 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@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index c6ba35df..450b1d5e 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml
index e8aafe44..537529bc 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template_version_comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.gitpod.yml b/.gitpod.yml
index 46118637..83599f63 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -6,12 +6,5 @@ tasks:
       nextflow self-update
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
-    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - nextflow.nextflow # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+  extensions:
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack
diff --git a/.nf-core.yml b/.nf-core.yml
index 4267fd77..eb1f60b7 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,8 +1,6 @@
-bump_version: null
 lint:
   actions_ci: false
-nf_core_version: 3.0.2
-org_path: null
+nf_core_version: 3.1.0
 repository_type: pipeline
 template:
   author: Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James
@@ -13,6 +11,4 @@ template:
   name: funcscan
   org: nf-core
   outdir: .
-  skip_features: null
   version: 2.1.0dev
-update: null
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 00000000..a33b527c
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "markdown.styles": ["public/vscode_markdown.css"]
+}
diff --git a/conf/base.config b/conf/base.config
index 9c812893..d4119475 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -20,7 +20,7 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
diff --git a/conf/modules.config b/conf/modules.config
index d266a387..d203d2b6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,6 +21,7 @@ process {
     withName: FASTQC {
         ext.args = '--quiet'
     }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
diff --git a/docs/usage.md b/docs/usage.md
index 0964dc6a..fe73ac87 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-:::warning
-Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-:::
+> [!WARNING]
+> Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -106,23 +105,21 @@ nextflow pull nf-core/funcscan
 
 ### Reproducibility
 
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
 First, go to the [nf-core/funcscan releases page](https://github.com/nf-core/funcscan/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-:::tip
-If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-:::
+> [!TIP]
+> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
 
 ## Core Nextflow arguments
 
-:::note
-These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
-:::
+> [!NOTE]
+> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen)
 
 ### `-profile`
 
@@ -130,16 +127,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-:::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-:::
+> [!IMPORTANT]
+> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.
 
-If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
+If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment.
 
 - `test`
   - A profile with a complete configuration for automated testing
@@ -175,13 +171,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se
 
 ### Resource requests
 
-Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
+Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
 
 To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
 
 ### Custom Containers
 
-In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date.
+In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date.
 
 To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
 
diff --git a/modules.json b/modules.json
index cfc0ad65..46bda8fd 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -21,17 +21,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index d8989f48..752c3a10 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -24,7 +24,7 @@ process FASTQC {
     // Make list of old name and new name pairs to use for renaming in the bash while loop
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
 
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4827da7a..2b2e62b8 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,6 +11,7 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
diff --git a/nextflow.config b/nextflow.config
index c9f36266..0691259a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -38,8 +38,7 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-
-    // Config options
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
     config_profile_name        = null
     config_profile_description = null
 
@@ -153,6 +152,13 @@ profiles {
         executor.name           = 'local'
         executor.cpus           = 4
         executor.memory         = 8.GB
+        process {
+            resourceLimits = [
+                memory: 8.GB,
+                cpus  : 4,
+                time  : 1.h
+            ]
+        }
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
@@ -201,30 +207,73 @@ set -C # No clobber - prevent output redirection from overwriting files.
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
 
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
 }
 report {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
 }
 trace {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
 }
 
 manifest {
     name            = 'nf-core/funcscan'
-    author          = """Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates"""
+    author          = """Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
+    contributors    = [
+        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
+        [
+            name: 'Jasmin Frangenberg',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        [
+            name: ' Anan Ibrahim',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        [
+            name: ' Louisa Perelo',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        [
+            name: ' Moritz E. Beber',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+        [
+            name: ' James A. Fellows Yates',
+            affiliation: '',
+            email: '',
+            github: '',
+            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: ''
+        ],
+    ]
     homePage        = 'https://github.com/nf-core/funcscan'
     description     = """Pipeline for screening for functional components of assembled contigs"""
     mainScript      = 'main.nf'
+    defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
     version         = '2.1.0dev'
     doi             = ''
@@ -237,9 +286,10 @@ plugins {
 
 validation {
     defaultIgnoreParams = ["genomes"]
+    monochromeLogs = params.monochrome_logs
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run nf-core/funcscan -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         beforeText = """
@@ -249,15 +299,15 @@ validation {
 \033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
 \033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                         \033[0;32m`._,._,\'\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+\033[0;35m  nf-core/funcscan ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/nf-core/funcscan/blob/master/CITATIONS.md
 """
     }
     summary {
@@ -265,6 +315,3 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e536a9d2..60a71c78 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -218,6 +218,12 @@
                     "description": "Base URL or local path to location of pipeline test dataset files",
                     "default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
                     "hidden": true
+                },
+                "trace_report_suffix": {
+                    "type": "string",
+                    "fa_icon": "far calendar",
+                    "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
+                    "hidden": true
                 }
             }
         }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
new file mode 100644
index 00000000..585014ae
--- /dev/null
+++ b/ro-crate-metadata.json
@@ -0,0 +1,324 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "creativeWorkStatus": "InProgress",
+            "datePublished": "2024-12-12T11:23:38+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-funcscan_logo_dark.png\">\n    <img alt=\"nf-core/funcscan\" src=\"docs/images/nf-core-funcscan_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/funcscan/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/funcscan/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/funcscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/funcscan/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/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/funcscan)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23funcscan-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/funcscan)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/funcscan** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/funcscan \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/funcscan/output).\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#funcscan` channel](https://nfcore.slack.com/channels/funcscan) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/funcscan for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "hasPart": [
+                {
+                    "@id": "main.nf"
+                },
+                {
+                    "@id": "assets/"
+                },
+                {
+                    "@id": "conf/"
+                },
+                {
+                    "@id": "docs/"
+                },
+                {
+                    "@id": "docs/images/"
+                },
+                {
+                    "@id": "modules/"
+                },
+                {
+                    "@id": "modules/nf-core/"
+                },
+                {
+                    "@id": "workflows/"
+                },
+                {
+                    "@id": "subworkflows/"
+                },
+                {
+                    "@id": "nextflow.config"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "nextflow_schema.json"
+                },
+                {
+                    "@id": "CHANGELOG.md"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "CODE_OF_CONDUCT.md"
+                },
+                {
+                    "@id": "CITATIONS.md"
+                },
+                {
+                    "@id": "modules.json"
+                },
+                {
+                    "@id": "docs/usage.md"
+                },
+                {
+                    "@id": "docs/output.md"
+                },
+                {
+                    "@id": ".nf-core.yml"
+                },
+                {
+                    "@id": ".pre-commit-config.yaml"
+                },
+                {
+                    "@id": ".prettierignore"
+                }
+            ],
+            "isBasedOn": "https://github.com/nf-core/funcscan",
+            "license": "MIT",
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "mentions": [
+                {
+                    "@id": "#81e54547-4c56-4a55-8ebc-88d7333cd8f9"
+                }
+            ],
+            "name": "nf-core/funcscan"
+        },
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                {
+                    "@id": "https://w3id.org/ro/crate/1.1"
+                },
+                {
+                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
+                }
+            ]
+        },
+        {
+            "@id": "main.nf",
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "creator": [
+                {
+                    "@id": "#jfy133@gmail.com"
+                }
+            ],
+            "dateCreated": "",
+            "dateModified": "2024-12-12T11:23:38Z",
+            "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "amp",
+                "amr",
+                "antibiotic-resistance",
+                "antimicrobial-peptides",
+                "antimicrobial-resistance-genes",
+                "arg",
+                "assembly",
+                "bgc",
+                "biosynthetic-gene-clusters",
+                "contigs",
+                "function",
+                "metagenomics",
+                "natural-products",
+                "screening",
+                "secondary-metabolites"
+            ],
+            "license": ["MIT"],
+            "name": ["nf-core/funcscan"],
+            "programmingLanguage": {
+                "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
+            },
+            "sdPublisher": {
+                "@id": "https://nf-co.re/"
+            },
+            "url": ["https://github.com/nf-core/funcscan", "https://nf-co.re/funcscan/dev/"],
+            "version": ["2.1.0dev"]
+        },
+        {
+            "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
+            "@type": "ComputerLanguage",
+            "identifier": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "name": "Nextflow",
+            "url": {
+                "@id": "https://www.nextflow.io/"
+            },
+            "version": "!>=24.04.2"
+        },
+        {
+            "@id": "#81e54547-4c56-4a55-8ebc-88d7333cd8f9",
+            "@type": "TestSuite",
+            "instance": [
+                {
+                    "@id": "#9b92794c-5ba0-4816-8b18-0346b8e4fefd"
+                }
+            ],
+            "mainEntity": {
+                "@id": "main.nf"
+            },
+            "name": "Test suite for nf-core/funcscan"
+        },
+        {
+            "@id": "#9b92794c-5ba0-4816-8b18-0346b8e4fefd",
+            "@type": "TestInstance",
+            "name": "GitHub Actions workflow for testing nf-core/funcscan",
+            "resource": "repos/nf-core/funcscan/actions/workflows/ci.yml",
+            "runsOn": {
+                "@id": "https://w3id.org/ro/terms/test#GithubService"
+            },
+            "url": "https://api.github.com"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#GithubService",
+            "@type": "TestService",
+            "name": "Github Actions",
+            "url": {
+                "@id": "https://github.com"
+            }
+        },
+        {
+            "@id": "assets/",
+            "@type": "Dataset",
+            "description": "Additional files"
+        },
+        {
+            "@id": "conf/",
+            "@type": "Dataset",
+            "description": "Configuration files"
+        },
+        {
+            "@id": "docs/",
+            "@type": "Dataset",
+            "description": "Markdown files for documenting the pipeline"
+        },
+        {
+            "@id": "docs/images/",
+            "@type": "Dataset",
+            "description": "Images for the documentation files"
+        },
+        {
+            "@id": "modules/",
+            "@type": "Dataset",
+            "description": "Modules used by the pipeline"
+        },
+        {
+            "@id": "modules/nf-core/",
+            "@type": "Dataset",
+            "description": "nf-core modules"
+        },
+        {
+            "@id": "workflows/",
+            "@type": "Dataset",
+            "description": "Main pipeline workflows to be executed in main.nf"
+        },
+        {
+            "@id": "subworkflows/",
+            "@type": "Dataset",
+            "description": "Smaller subworkflows"
+        },
+        {
+            "@id": "nextflow.config",
+            "@type": "File",
+            "description": "Main Nextflow configuration file"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File",
+            "description": "Basic pipeline usage information"
+        },
+        {
+            "@id": "nextflow_schema.json",
+            "@type": "File",
+            "description": "JSON schema for pipeline parameter specification"
+        },
+        {
+            "@id": "CHANGELOG.md",
+            "@type": "File",
+            "description": "Information on changes made to the pipeline"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File",
+            "description": "The license - should be MIT"
+        },
+        {
+            "@id": "CODE_OF_CONDUCT.md",
+            "@type": "File",
+            "description": "The nf-core code of conduct"
+        },
+        {
+            "@id": "CITATIONS.md",
+            "@type": "File",
+            "description": "Citations needed when using the pipeline"
+        },
+        {
+            "@id": "modules.json",
+            "@type": "File",
+            "description": "Version information for modules from nf-core/modules"
+        },
+        {
+            "@id": "docs/usage.md",
+            "@type": "File",
+            "description": "Usage documentation"
+        },
+        {
+            "@id": "docs/output.md",
+            "@type": "File",
+            "description": "Output documentation"
+        },
+        {
+            "@id": ".nf-core.yml",
+            "@type": "File",
+            "description": "nf-core configuration file, configuring template features and linting rules"
+        },
+        {
+            "@id": ".pre-commit-config.yaml",
+            "@type": "File",
+            "description": "Configuration file for pre-commit hooks"
+        },
+        {
+            "@id": ".prettierignore",
+            "@type": "File",
+            "description": "Ignore file for prettier"
+        },
+        {
+            "@id": "https://nf-co.re/",
+            "@type": "Organization",
+            "name": "nf-core",
+            "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#jfy133@gmail.com",
+            "@type": "Person",
+            "email": "jfy133@gmail.com",
+            "name": "James Fellows Yates"
+        }
+    ]
+}
diff --git a/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf b/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
index 7264f1d4..5693c827 100644
--- a/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
@@ -116,7 +116,8 @@ workflow PIPELINE_COMPLETION {
 
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-
+    def multiqc_reports = multiqc_report.toList()
+    
     //
     // Completion email and summary
     //
@@ -129,7 +130,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_reports.getVal(),
             )
         }
 
@@ -225,7 +226,7 @@ def toolBibliographyText() {
 }
 
 def methodsDescriptionText(mqc_methods_yaml) {
-    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
+    // Convert  to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file
     def meta = [:]
     meta.workflow = workflow.toMap()
     meta["manifest_map"] = workflow.manifest.toMap()
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index 0fcbf7b3..d6e593e8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -92,10 +92,12 @@ def checkCondaChannels() {
         channels = config.channels
     }
     catch (NullPointerException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
     catch (IOException e) {
+        log.debug(e)
         log.warn("Could not verify conda channel configuration.")
         return null
     }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index ca964ce8..02dbf094 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -52,10 +52,12 @@ nextflow_workflow {
         }
 
         then {
-            assertAll(
-                { assert workflow.success },
-                { assert workflow.stdout.contains("nextflow_workflow v9.9.9") }
-            )
+            expect {
+                with(workflow) {
+                    assert success
+                    assert "nextflow_workflow v9.9.9" in stdout
+                }
+            }
         }
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 5cb7bafe..bfd25876 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) {
     }
 }
 
-//
-// Citation string for pipeline
-//
-def workflowCitation() {
-    def temp_doi_ref = ""
-    def manifest_doi = workflow.manifest.doi.tokenize(",")
-    // Handling multiple DOIs
-    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
-    // Removing ` ` since the manifest.doi is a string and not a proper list
-    manifest_doi.each { doi_ref ->
-        temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
-    }
-    return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + "  https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
-}
-
 //
 // Generate workflow version string
 //
@@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) {
     return yaml_file_text
 }
 
-//
-// nf-core logo
-//
-def nfCoreLogo(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    String.format(
-        """\n
-        ${dashedLine(monochrome_logs)}
-                                                ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
-        ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
-        ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
-        ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                ${colors.green}`._,._,\'${colors.reset}
-        ${colors.purple}  ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset}
-        ${dashedLine(monochrome_logs)}
-        """.stripIndent()
-    )
-}
-
-//
-// Return dashed line
-//
-def dashedLine(monochrome_logs=true) {
-    def colors = logColours(monochrome_logs) as Map
-    return "-${colors.dim}----------------------------------------------------${colors.reset}-"
-}
-
 //
 // ANSII colours used for terminal logging
 //
@@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) {
     return colorcodes
 }
 
-//
-// Attach the multiqc report to email
-//
-def attachMultiqcReport(multiqc_report) {
-    def mqc_report = null
-    try {
-        if (workflow.success) {
-            mqc_report = multiqc_report.getVal()
-            if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
-                if (mqc_report.size() > 1) {
-                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                }
-                mqc_report = mqc_report[0]
-            }
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
         }
+    } else {
+        return null
     }
-    catch (Exception all) {
-        if (multiqc_report) {
-            log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email")
-        }
-    }
-    return mqc_report
 }
 
 //
@@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     email_fields['summary']      = summary << misc_fields
 
     // On success try attach the multiqc report
-    def mqc_report = attachMultiqcReport(multiqc_report)
+    def mqc_report = getSingleReport(multiqc_report)
 
     // Check if we are only sending emails on failure
     def email_address = email
@@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def email_html    = html_template.toString()
 
     // Render the sendmail template
-    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
     def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
     def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
     def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
@@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     if (email_address) {
         try {
             if (plaintext_email) {
-new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')            }
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
             ['sendmail', '-t'].execute() << sendmail_html
             log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
         }
-        catch (Exception all) {
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
             // Catch failures and try with plaintext
             def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
             mail_cmd.execute() << email_html
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
index 1dc317f8..f117040c 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -41,26 +41,14 @@ nextflow_function {
         }
     }
 
-    test("Test Function workflowCitation") {
-
-        function "workflowCitation"
-
-        then {
-            assertAll(
-                { assert function.success },
-                { assert snapshot(function.result).match() }
-            )
-        }
-    }
-
-    test("Test Function nfCoreLogo") {
+    test("Test Function without logColours") {
 
-        function "nfCoreLogo"
+        function "logColours"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = true
                 """
             }
         }
@@ -73,9 +61,8 @@ nextflow_function {
         }
     }
 
-    test("Test Function dashedLine") {
-
-        function "dashedLine"
+    test("Test Function with logColours") {
+        function "logColours"
 
         when {
             function {
@@ -93,14 +80,13 @@ nextflow_function {
         }
     }
 
-    test("Test Function without logColours") {
-
-        function "logColours"
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = true
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
                 """
             }
         }
@@ -108,18 +94,22 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") }
             )
         }
     }
 
-    test("Test Function with logColours") {
-        function "logColours"
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
 
         when {
             function {
                 """
-                input[0] = false
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -127,7 +117,9 @@ nextflow_function {
         then {
             assertAll(
                 { assert function.success },
-                { assert snapshot(function.result).match() }
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
             )
         }
     }
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 1037232c..02c67014 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -17,26 +17,6 @@
         },
         "timestamp": "2024-02-28T12:02:59.729647"
     },
-    "Test Function nfCoreLogo": {
-        "content": [
-            "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:10.562934"
-    },
-    "Test Function workflowCitation": {
-        "content": [
-            "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:07.019761"
-    },
     "Test Function without logColours": {
         "content": [
             {
@@ -95,16 +75,6 @@
         },
         "timestamp": "2024-02-28T12:03:17.969323"
     },
-    "Test Function dashedLine": {
-        "content": [
-            "-\u001b[2m----------------------------------------------------\u001b[0m-"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T12:03:14.366181"
-    },
     "Test Function with logColours": {
         "content": [
             {
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
index 842dc432..8fb30164 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
@@ -94,7 +94,7 @@ nextflow_workflow {
 
             params {
                 test_data   = ''
-                outdir      = 1
+                outdir      = null
             }
 
             workflow {
diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf
index 8a25159c..fafc69bf 100644
--- a/workflows/funcscan.nf
+++ b/workflows/funcscan.nf
@@ -39,7 +39,7 @@ workflow FUNCSCAN {
     softwareVersionsToYAML(ch_versions)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
-            name: 'nf_core_'  + 'pipeline_software_' +  'mqc_'  + 'versions.yml',
+            name: 'nf_core_'  +  'funcscan_software_'  + 'mqc_'  + 'versions.yml',
             sort: true,
             newLine: true
         ).set { ch_collated_versions }

From 74b73e91e2bd09588613f98e0a56e3c12b45c06a Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Wed, 18 Dec 2024 11:25:09 +0100
Subject: [PATCH 2/8] Add contributor information

---
 nextflow.config | 46 +++++++++++++++++++++++-----------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 0691259a..31df8edd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -231,43 +231,43 @@ manifest {
         // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
             name: 'Jasmin Frangenberg',
-            affiliation: '',
-            email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
+            email: 'jasmin.frangenberg@leibniz-hki.de',
+            github: 'jasmezz',
+            contribution: [author, maintainer], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0009-0004-5961-4709'
         ],
         [
             name: ' Anan Ibrahim',
-            affiliation: '',
-            email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
+            email: 'anan.ibrahim@leibniz-hki.de',
+            github: 'darcy220606',
+            contribution: [author, maintainer], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0000-0003-3719-901X'
         ],
         [
             name: ' Louisa Perelo',
-            affiliation: '',
-            email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
+            email: 'louisa.perelo@qbic.uni-tuebingen.de',
+            github: 'louperelo',
+            contribution: [author, contributor], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0000-0002-7307-062X'
         ],
         [
             name: ' Moritz E. Beber',
             affiliation: '',
             email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            github: 'Midnighter',
+            contribution: [author, contributor], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0000-0003-2406-1978'
         ],
         [
             name: ' James A. Fellows Yates',
-            affiliation: '',
-            email: '',
-            github: '',
-            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
-            orcid: ''
+            affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
+            email: 'james_fellows_yates@eva.mpg.de',
+            github: 'jfy133',
+            contribution: [author, maintainer], // List of contribution types ('author', 'maintainer' or 'contributor')
+            orcid: '0000-0001-5585-6277'
         ],
     ]
     homePage        = 'https://github.com/nf-core/funcscan'

From 867c9be17743540bf708512c55f778ebef56d2f5 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 19 Dec 2024 11:34:36 +0100
Subject: [PATCH 3/8] Fix tests

---
 nextflow.config                       | 13 ++++++++-----
 tests/test.nf.test                    |  2 +-
 tests/test_bakta.nf.test              |  2 +-
 tests/test_bgc_bakta.nf.test          |  2 +-
 tests/test_bgc_prokka.nf.test         |  2 +-
 tests/test_bgc_pyrodigal.nf.test      |  2 +-
 tests/test_full.nf.test               |  2 +-
 tests/test_nothing.nf.test            |  2 +-
 tests/test_preannotated.nf.test       |  2 +-
 tests/test_preannotated_bgc.nf.test   |  2 +-
 tests/test_prokka.nf.test             |  2 +-
 tests/test_taxonomy_bakta.nf.test     |  2 +-
 tests/test_taxonomy_prokka.nf.test    |  2 +-
 tests/test_taxonomy_pyrodigal.nf.test |  2 +-
 14 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d7f5e1d4..1622a6f7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -468,7 +468,7 @@ manifest {
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
             email: 'jasmin.frangenberg@leibniz-hki.de',
             github: 'jasmezz',
-            contribution: [author, maintainer],
+            contribution: ['author', 'maintainer'],
             orcid: '0009-0004-5961-4709',
         ],
         [
@@ -476,7 +476,7 @@ manifest {
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
             email: 'anan.ibrahim@leibniz-hki.de',
             github: 'darcy220606',
-            contribution: [author, maintainer],
+            contribution: ['author', 'maintainer'],
             orcid: '0000-0003-3719-901X',
         ],
         [
@@ -484,7 +484,7 @@ manifest {
             affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
             email: 'louisa.perelo@qbic.uni-tuebingen.de',
             github: 'louperelo',
-            contribution: [author, contributor],
+            contribution: ['author', 'contributor'],
             orcid: '0000-0002-7307-062X',
         ],
         [
@@ -492,7 +492,7 @@ manifest {
             affiliation: '',
             email: '',
             github: 'Midnighter',
-            contribution: [author, contributor],
+            contribution: ['author', 'contributor'],
             orcid: '0000-0003-2406-1978',
         ],
         [
@@ -500,7 +500,7 @@ manifest {
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
             email: 'james_fellows_yates@eva.mpg.de',
             github: 'jfy133',
-            contribution: [author, maintainer],
+            contribution: ['author', 'maintainer'],
             orcid: '0000-0001-5585-6277',
         ],
     ]
@@ -549,3 +549,6 @@ validation {
         afterText  = validation.help.afterText
     }
 }
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
diff --git a/tests/test.nf.test b/tests/test.nf.test
index 28e088b5..6ffdd1a0 100644
--- a/tests/test.nf.test
+++ b/tests/test.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // AMPir
diff --git a/tests/test_bakta.nf.test b/tests/test_bakta.nf.test
index b1913b04..c040b2ab 100644
--- a/tests/test_bakta.nf.test
+++ b/tests/test_bakta.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // AMPir
diff --git a/tests/test_bgc_bakta.nf.test b/tests/test_bgc_bakta.nf.test
index 37a0a0b1..3debacd6 100644
--- a/tests/test_bgc_bakta.nf.test
+++ b/tests/test_bgc_bakta.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // antiSMASH
diff --git a/tests/test_bgc_prokka.nf.test b/tests/test_bgc_prokka.nf.test
index 0fe53cd5..f415a95b 100644
--- a/tests/test_bgc_prokka.nf.test
+++ b/tests/test_bgc_prokka.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // antiSMASH
diff --git a/tests/test_bgc_pyrodigal.nf.test b/tests/test_bgc_pyrodigal.nf.test
index cab97577..24ecaeb3 100644
--- a/tests/test_bgc_pyrodigal.nf.test
+++ b/tests/test_bgc_pyrodigal.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // antiSMASH
diff --git a/tests/test_full.nf.test b/tests/test_full.nf.test
index b5d53e6d..28b893de 100644
--- a/tests/test_full.nf.test
+++ b/tests/test_full.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // AMP workflow
diff --git a/tests/test_nothing.nf.test b/tests/test_nothing.nf.test
index a141d401..01a0ebc9 100644
--- a/tests/test_nothing.nf.test
+++ b/tests/test_nothing.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
             )
         }
diff --git a/tests/test_preannotated.nf.test b/tests/test_preannotated.nf.test
index 32a86ac4..f13676b8 100644
--- a/tests/test_preannotated.nf.test
+++ b/tests/test_preannotated.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // AMPir
diff --git a/tests/test_preannotated_bgc.nf.test b/tests/test_preannotated_bgc.nf.test
index 0e9ca618..f6f291fb 100644
--- a/tests/test_preannotated_bgc.nf.test
+++ b/tests/test_preannotated_bgc.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // antiSMASH
diff --git a/tests/test_prokka.nf.test b/tests/test_prokka.nf.test
index 94e65ae2..d332362e 100644
--- a/tests/test_prokka.nf.test
+++ b/tests/test_prokka.nf.test
@@ -17,7 +17,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // AMPir
diff --git a/tests/test_taxonomy_bakta.nf.test b/tests/test_taxonomy_bakta.nf.test
index 5a412fa9..6498c4bd 100644
--- a/tests/test_taxonomy_bakta.nf.test
+++ b/tests/test_taxonomy_bakta.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // ampir
diff --git a/tests/test_taxonomy_prokka.nf.test b/tests/test_taxonomy_prokka.nf.test
index e0992dbf..0628508a 100644
--- a/tests/test_taxonomy_prokka.nf.test
+++ b/tests/test_taxonomy_prokka.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // ampir
diff --git a/tests/test_taxonomy_pyrodigal.nf.test b/tests/test_taxonomy_pyrodigal.nf.test
index 3cc5535e..8f325fc0 100644
--- a/tests/test_taxonomy_pyrodigal.nf.test
+++ b/tests/test_taxonomy_pyrodigal.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
+                { assert new File("$outputDir/pipeline_info/nf_core_funcscan_software_mqc_versions.yml").exists() },
                 { assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
 
                 // ampir

From 46b73e88ed02096a37da61dd11401bafb41c981f Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 19 Dec 2024 11:42:53 +0100
Subject: [PATCH 4/8] Update
 subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf

---
 subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf b/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
index d2093d01..b6ff2df8 100644
--- a/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
@@ -99,7 +99,6 @@ workflow PIPELINE_COMPLETION {
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
     def multiqc_reports = multiqc_report.toList()
-    
     //
     // Completion email and summary
     //

From 423d466339bd87a5c860ef9ac4763dd961d61861 Mon Sep 17 00:00:00 2001
From: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
Date: Thu, 19 Dec 2024 12:01:21 +0000
Subject: [PATCH 5/8] Update author details [skip ci]

---
 nextflow.config | 42 +++++++++++++++++++++++++-----------------
 1 file changed, 25 insertions(+), 17 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 1622a6f7..1154deb2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -467,41 +467,49 @@ manifest {
             name: 'Jasmin Frangenberg',
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
             email: 'jasmin.frangenberg@leibniz-hki.de',
-            github: 'jasmezz',
+            github: 'https://github.com/jasmezz',
             contribution: ['author', 'maintainer'],
-            orcid: '0009-0004-5961-4709',
+            orcid: 'https://orcid.org/0009-0004-5961-4709',
         ],
         [
-            name: ' Anan Ibrahim',
+            name: 'Anan Ibrahim',
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany',
-            email: 'anan.ibrahim@leibniz-hki.de',
-            github: 'darcy220606',
+            email: '',
+            github: 'https://github.com/darcy220606',
             contribution: ['author', 'maintainer'],
-            orcid: '0000-0003-3719-901X',
+            orcid: 'https://orcid.org/0000-0003-3719-901X',
         ],
         [
-            name: ' Louisa Perelo',
+            name: 'Louisa Perelo',
             affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
-            email: 'louisa.perelo@qbic.uni-tuebingen.de',
-            github: 'louperelo',
+            email: '',
+            github: 'https://github.com/louperelo',
             contribution: ['author', 'contributor'],
-            orcid: '0000-0002-7307-062X',
+            orcid: 'https://orcid.org/0000-0002-7307-062X',
         ],
         [
-            name: ' Moritz E. Beber',
-            affiliation: '',
+            name: 'Moritz E. Beber',
+            affiliation: 'Unseen Bio ApS, Copenhagen, Denmark',
             email: '',
             github: 'Midnighter',
             contribution: ['author', 'contributor'],
-            orcid: '0000-0003-2406-1978',
+            orcid: 'https://orcid.org/0000-0003-2406-1978',
         ],
         [
-            name: ' James A. Fellows Yates',
+            name: 'James A. Fellows Yates',
             affiliation: 'Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany',
-            email: 'james_fellows_yates@eva.mpg.de',
-            github: 'jfy133',
+            email: '',
+            github: 'https://github.com/jfy133',
             contribution: ['author', 'maintainer'],
-            orcid: '0000-0001-5585-6277',
+            orcid: 'https://orcid.org/0000-0001-5585-6277',
+        ],
+        [
+            name: 'Vedanth Ramji',
+            affiliation: 'Big Data Biology Lab, Chennai, India',
+            email: '',
+            github: 'https://github.com/Vedanth-Ramji',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0009-0001-5311-7611',
         ],
     ]
     homePage        = 'https://github.com/nf-core/funcscan'

From 218ca0cf49adb13bb7052ae929cf0eab2d98b951 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 19 Dec 2024 13:28:11 +0100
Subject: [PATCH 6/8] Update docs/usage.md

Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
---
 docs/usage.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 9fc5bca5..9b66fd2b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -544,7 +544,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli
 > [!IMPORTANT]
 > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 
-The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
+The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
 Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important!
 They are loaded in sequence, so later profiles can overwrite earlier profiles.

From c0967e94d592d979c5d6904ff7f72d238f2890b1 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 19 Dec 2024 13:50:27 +0100
Subject: [PATCH 7/8] Update nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 1154deb2..8a700a13 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -505,7 +505,7 @@ manifest {
         ],
         [
             name: 'Vedanth Ramji',
-            affiliation: 'Big Data Biology Lab, Chennai, India',
+            affiliation: 'Queensland University of Technology, Brisbane, Australia',
             email: '',
             github: 'https://github.com/Vedanth-Ramji',
             contribution: ['contributor'],

From f364d6f71d2e2cd741f350d3f09e54717935ff6e Mon Sep 17 00:00:00 2001
From: jasmezz <jasmin.frangenberg@hki-jena.de>
Date: Thu, 19 Dec 2024 14:01:24 +0100
Subject: [PATCH 8/8] Remove vscode file

---
 .vscode/settings.json | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
deleted file mode 100644
index a33b527c..00000000
--- a/.vscode/settings.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "markdown.styles": ["public/vscode_markdown.css"]
-}