From 530f4cbf4fd7caa19b37b9fd6143acae9a336202 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 24 Jul 2026 12:36:30 +0000
Subject: [PATCH 1/3] Template update for nf-core/tools version 4.0.3

---
 .github/actions/nf-test/action.yml            |  2 +-
 .github/workflows/branch.yml                  | 60 +++++++++-----
 .github/workflows/linting.yml                 | 18 ++++
 .github/workflows/linting_comment.yml         | 28 -------
 .github/workflows/nf-test.yml                 | 57 +++++++++++++
 .github/workflows/pr-comment.yml              | 82 +++++++++++++++++++
 .github/workflows/release-announcements.yml   |  2 +-
 .../workflows/template-version-comment.yml    | 56 ++++++++-----
 .nf-core.yml                                  |  2 +-
 README.md                                     |  2 +-
 ro-crate-metadata.json                        | 18 ++--
 11 files changed, 243 insertions(+), 84 deletions(-)
 delete mode 100644 .github/workflows/linting_comment.yml
 create mode 100644 .github/workflows/pr-comment.yml

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index ad686e8..945c56f 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
+      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 16fb23e..331ba11 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -2,11 +2,13 @@ name: nf-core branch protection
 # 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:
+  pull_request:
     branches:
       - main
       - master
 
+permissions: {}
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -14,33 +16,47 @@ jobs:
       # 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/spatialvi'
+        env:
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialvi ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ "$HEAD_REPO" == nf-core/spatialvi ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
-      # If the above check failed, post a comment on the PR explaining the failure
-      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
-      - name: Post PR comment
+      # If the above check failed, build a comment to be posted by the shared poster workflow
+      - name: Build PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
-        with:
-          message: |
-            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          BASE_REF: ${{ github.event.pull_request.base.ref }}
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
+          PR_USER: ${{ github.event.pull_request.user.login }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "branch" > pr-comment/header.txt
+          cat > pr-comment/comment.md <<EOF
+          ## This PR is against the \`${BASE_REF}\` branch :x:
 
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
+          * Do not close this PR
+          * Click _Edit_ and change the \`base\` to \`dev\`
+          * This CI test will remain failed until you push a new commit
 
-            ---
+          ---
 
-            Hi @${{ github.event.pull_request.user.login }},
+          Hi @${PR_USER},
 
-            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/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+          It looks like this pull-request is has been made against the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) ${BASE_REF} branch.
+          The ${BASE_REF} branch on nf-core repositories should always contain code from the latest release.
+          Because of this, PRs to ${BASE_REF} are only allowed if they come from the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) \`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.
+          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.
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+          Thanks again for your contribution!
+          EOF
+
+      - name: Upload PR comment artifact
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 8738ffc..bc32219 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -74,3 +74,21 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "lint" > pr-comment/header.txt
+          [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
deleted file mode 100644
index 5b0c24f..0000000
--- a/.github/workflows/linting_comment.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: nf-core linting comment
-# This workflow is triggered after the linting action is complete
-# It posts an automated comment to the PR, even if the PR is coming from a fork
-
-on:
-  workflow_run:
-    workflows: ["nf-core linting"]
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download lint results
-        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
-        with:
-          workflow: linting.yml
-          workflow_conclusion: completed
-
-      - name: Get PR number
-        id: pr_number
-        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
-
-      - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          number: ${{ steps.pr_number.outputs.pr_number }}
-          path: linting-logs/lint_results.md
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index efd72d6..4de681a 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -116,6 +116,22 @@ jobs:
             fi
           fi
 
+      # continue-on-error keeps latest-everything from failing the job, so it never shows up in
+      # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead;
+      # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those.
+      - name: Prepare PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        run: |
+          mkdir -p pr-comment-fragment
+          echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md
+
+      - name: Upload PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment-fragment-${{ strategy.job-index }}
+          path: pr-comment-fragment/
+
   confirm-pass:
     needs: [nf-test]
     if: always()
@@ -142,3 +158,44 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
+
+      - name: Download PR comment fragments
+        if: ${{ always() }}
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        continue-on-error: true
+        with:
+          pattern: pr-comment-fragment-*
+          path: pr-comment-fragments
+          merge-multiple: true
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR.
+      # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported.
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "nf-test" > pr-comment/header.txt
+          if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then
+            {
+              echo "## ❌ nf-test failed with latest Nextflow version"
+              echo ""
+              echo "> [!NOTE]"
+              echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure."
+              echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing."
+              echo ""
+              cat pr-comment-fragments/*.md
+              echo ""
+              echo "See the [full run](${RUN_URL}) for details."
+            } > pr-comment/comment.md
+          fi
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/pr-comment.yml b/.github/workflows/pr-comment.yml
new file mode 100644
index 0000000..ab7b59d
--- /dev/null
+++ b/.github/workflows/pr-comment.yml
@@ -0,0 +1,82 @@
+name: Post PR comment
+# Shared, privileged comment poster.
+#
+# This is the single workflow that runs with a write token. It is triggered
+# after any of the listed "producer" workflows complete on a pull request.
+# Each producer runs untrusted PR code (if any) with a read-only token and
+# uploads a `pr-comment` artifact describing the comment to post; this workflow
+# only ever reads that plain-text artifact, so no PR code is executed here.
+#
+# Artifact contract (uploaded by producers under the name `pr-comment`):
+#   pr_number.txt  - the pull request number
+#   header.txt     - sticky-comment identifier (keeps comment types separate)
+#   comment.md     - the Markdown body (omit the file to post nothing)
+
+on:
+  workflow_run:
+    workflows:
+      - "nf-core linting"
+      - "nf-core template version comment"
+      - "nf-core branch protection"
+      - "Run nf-test"
+
+permissions:
+  actions: read
+  contents: read
+  pull-requests: write
+
+jobs:
+  post-comment:
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request'
+    steps:
+      - name: Download PR comment artifact
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
+        with:
+          run_id: ${{ github.event.workflow_run.id }}
+          name: pr-comment
+          path: pr-comment
+          if_no_artifact_found: ignore
+
+      - name: Read comment metadata
+        id: meta
+        run: |
+          echo "::group::Downloaded pr-comment contents"
+          ls -la pr-comment 2>/dev/null || echo "No pr-comment/ directory was downloaded."
+          echo "::endgroup::"
+
+          if [ ! -d pr-comment ]; then
+            echo "No pr-comment artifact found; nothing to post."
+            exit 0
+          fi
+
+          if [ ! -f pr-comment/comment.md ]; then
+            echo "Artifact present but no comment.md; nothing to post."
+            exit 0
+          fi
+
+          pr_number=$(cat pr-comment/pr_number.txt)
+          header=$(cat pr-comment/header.txt)
+          echo "Found comment.md (header='$header', pr_number='$pr_number')."
+
+          # Guard against anything unexpected ending up in the PR number.
+          case "$pr_number" in
+            ''|*[!0-9]*)
+              echo "Invalid PR number: '$pr_number'"
+              exit 1
+              ;;
+          esac
+
+          echo "pr_number=$pr_number" >> "$GITHUB_OUTPUT"
+          echo "header=$header" >> "$GITHUB_OUTPUT"
+          echo "post=true" >> "$GITHUB_OUTPUT"
+          echo "Will post comment to PR #${pr_number}."
+
+      - name: Post PR comment
+        if: steps.meta.outputs.post == 'true'
+        uses: marocchino/sticky-pull-request-comment@5770ad5eb8f42dd2c4f34da00c94c5381e49af88 # v3.0.5
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          number: ${{ steps.meta.outputs.pr_number }}
+          header: ${{ steps.meta.outputs.header }}
+          path: pr-comment/comment.md
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 78d5dbe..4974f44 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
+      - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index ea30827..ee102f7 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -2,10 +2,13 @@ name: nf-core template version comment
 # This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
 # It posts a comment to the PR, even if it comes from a fork.
 
-on: pull_request_target
+on:
+  pull_request:
+
+permissions: {}
 
 jobs:
-  template_version:
+  check_template_version:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
@@ -22,25 +25,36 @@ jobs:
       - name: Install nf-core
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+          pip install nf-core
+
+      - name: Build PR comment if template is outdated
+        # The fork-controlled version is passed via the environment and only ever
+        # used as quoted shell data (never interpolated into a command), so it
+        # cannot be used for script injection.
+        env:
+          PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "template-version" > pr-comment/header.txt
+
+          latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1)
 
-      - name: Check nf-core outdated
-        id: nf_core_outdated
-        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
+          if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then
+            cat > pr-comment/comment.md <<EOF
+          > [!WARNING]
+          > Newer version of the nf-core template is available.
+          >
+          > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}.
+          > Please update your pipeline to the latest version.
+          >
+          > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
+          EOF
+          fi
 
-      - name: Post nf-core template version comment
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
-        if: |
-          contains(env.OUTPUT, 'nf-core')
+      - name: Upload PR comment artifact
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
-          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
-          allow-repeats: false
-          message: |
-            > [!WARNING]
-            > Newer version of the nf-core template is available.
-            >
-            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            > Please update your pipeline to the latest version.
-            >
-            > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
-          #
+          name: pr-comment
+          path: pr-comment/
diff --git a/.nf-core.yml b/.nf-core.yml
index be12807..4ee9291 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,7 +9,7 @@ lint:
     - assets/nf-core-spatialvi_logo_light.png
     - docs/images/nf-core-spatialvi_logo_light.png
     - docs/images/nf-core-spatialvi_logo_dark.png
-nf_core_version: 4.0.2
+nf_core_version: 4.0.3
 repository_type: pipeline
 template:
   author: Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj
diff --git a/README.md b/README.md
index 3337c4c..b0ae453 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 1080b93..78bd815 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-04-30T13:33:27+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialvi_logo_dark.png\">\n    <img alt=\"nf-core/spatialvi\" src=\"docs/images/nf-core-spatialvi_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialvi)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialvi/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialvi/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/spatialvi/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/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\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/spatialvi)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialvi-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialvi)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/spatialvi** 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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-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/spatialvi \\\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/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/spatialvi/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/spatialvi/output).\n\n## Credits\n\nnf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialvi` channel](https://nfcore.slack.com/channels/spatialvi) (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/spatialvi 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",
+            "datePublished": "2026-07-24T12:36:21+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialvi_logo_dark.png\">\n    <img alt=\"nf-core/spatialvi\" src=\"docs/images/nf-core-spatialvi_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialvi)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialvi/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialvi/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/spatialvi/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/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\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/spatialvi)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialvi-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialvi)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/spatialvi** 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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-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/spatialvi \\\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/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/spatialvi/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/spatialvi/output).\n\n## Credits\n\nnf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialvi` channel](https://nfcore.slack.com/channels/spatialvi) (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/spatialvi 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"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#d877e7ce-5827-4338-96a5-71caf0d7df23"
+                    "@id": "#943c68f0-8198-411c-bc67-2c4185d0bd3e"
                 }
             ],
             "name": "nf-core/spatialvi"
@@ -136,11 +136,11 @@
                     "@id": "https://orcid.org/0000-0002-3298-2358"
                 },
                 {
-                    "@id": "#56048f34-cab3-4158-9146-6f434210ef75"
+                    "@id": "#ef2d6ff5-4891-454d-b799-6123121c466b"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-04-30T13:33:27Z",
+            "dateModified": "2026-07-24T12:36:21Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -181,11 +181,11 @@
             "version": "!>=25.10.4"
         },
         {
-            "@id": "#d877e7ce-5827-4338-96a5-71caf0d7df23",
+            "@id": "#943c68f0-8198-411c-bc67-2c4185d0bd3e",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#55f34f96-6b35-461d-b395-fe19fd0a2d5b"
+                    "@id": "#1ebb83ae-7830-4731-9382-62769ca97ac1"
                 }
             ],
             "mainEntity": {
@@ -194,7 +194,7 @@
             "name": "Test suite for nf-core/spatialvi"
         },
         {
-            "@id": "#55f34f96-6b35-461d-b395-fe19fd0a2d5b",
+            "@id": "#1ebb83ae-7830-4731-9382-62769ca97ac1",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/spatialvi",
             "resource": "repos/nf-core/spatialvi/actions/workflows/nf-test.yml",
@@ -346,7 +346,7 @@
             "name": "Jeffrey Chuang"
         },
         {
-            "@id": "#56048f34-cab3-4158-9146-6f434210ef75",
+            "@id": "#ef2d6ff5-4891-454d-b799-6123121c466b",
             "@type": "Person",
             "name": "Anuj Srivastava"
         }

From 534dac8314299f4b3cc3d2988d10b67998b0ca3e Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 1 Sep 2026 13:07:13 +0000
Subject: [PATCH 2/3] Template update for nf-core/tools version 4.1.0

---
 .github/actions/nf-test/action.yml            |    6 +-
 .github/workflows/clean-up.yml                |    2 +-
 .github/workflows/download_pipeline.yml       |    6 +-
 .github/workflows/fix_linting.yml             |    6 +-
 .github/workflows/linting.yml                 |   16 +-
 .github/workflows/nf-test.yml                 |    4 +-
 .../workflows/template-version-comment.yml    |    2 +-
 .hooks/block_pipeline_outdir.sh               |   44 +
 .nf-core.yml                                  |    5 +-
 .pre-commit-config.yaml                       |   19 +-
 CHANGELOG.md                                  |    2 +-
 README.md                                     |    2 +-
 conf/base.config                              |    3 +
 conf/containers_conda_lock_files_amd64.config |    4 +-
 conf/containers_conda_lock_files_arm64.config |    4 +-
 conf/containers_docker_amd64.config           |    2 +-
 conf/containers_docker_arm64.config           |    2 +-
 .../containers_singularity_https_amd64.config |    2 +-
 .../containers_singularity_https_arm64.config |    2 +-
 conf/containers_singularity_oras_amd64.config |    2 +-
 conf/containers_singularity_oras_arm64.config |    2 +-
 conf/modules.config                           |    3 +-
 docs/CONTRIBUTING.md                          |    8 +-
 docs/output.md                                |    2 +-
 docs/usage.md                                 |    2 +-
 modules.json                                  |    6 +-
 .../linux_amd64-bd-c17fb751507e9dfc_1.txt     | 1526 +++++++++++++++++
 .../linux_arm64-bd-5c84a5000a226ab5_1.txt     | 1476 ++++++++++++++++
 modules/nf-core/multiqc/environment.yml       |    2 +-
 modules/nf-core/multiqc/main.nf               |    4 +-
 modules/nf-core/multiqc/meta.yml              |   28 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   |   10 +-
 ro-crate-metadata.json                        |   18 +-
 .../utils_nfcore_spatialvi_pipeline/main.nf   |    3 +-
 .../nf-core/utils_nfschema_plugin/main.nf     |   12 +-
 .../nf-core/utils_nfschema_plugin/meta.yml    |   24 +
 .../utils_nfschema_plugin/tests/main.nf.test  |    5 +
 .../tests/nextflow.config                     |    2 +-
 tests/nextflow.config                         |    5 +-
 39 files changed, 3188 insertions(+), 85 deletions(-)
 create mode 100755 .hooks/block_pipeline_outdir.sh
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
 create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 945c56f..4175e3c 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -20,12 +20,12 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
       with:
         python-version: "3.14"
 
@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 172de6f..b694012 100644
--- a/.github/workflows/clean-up.yml
+++ b/.github/workflows/clean-up.yml
@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index a7bf4fc..ca2eb82 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -39,15 +39,15 @@ jobs:
     needs: configure
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 20e51bd..87dfacf 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@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,12 +32,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         continue-on-error: true
 
       # indication that the linting has finished
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index bc32219..277f12f 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,30 +11,30 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
@@ -46,7 +46,7 @@ jobs:
         run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
+        if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 4de681a..e363215 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -85,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index ee102f7..149e285 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh
new file mode 100755
index 0000000..e9ba4f9
--- /dev/null
+++ b/.hooks/block_pipeline_outdir.sh
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# This hook is used to block commits if they include staged files inside a directory
+# which also contains a subdirectory called `pipeline_info`. The purpose of this is to
+# prevent users from inadvertently committing output from pipeline test runs inside the
+# development directory.
+
+set -e
+
+status=0
+seen_dirs=""
+
+while IFS= read -r file; do
+    # The offending output bundle's root is the ancestor directory that has
+    # `pipeline_info` as an immediate child, so callers can restore it in one go.
+    if [[ "$file" == pipeline_info/* ]]; then
+        top_dir="pipeline_info"
+    elif [[ "$file" == */pipeline_info/* ]]; then
+        top_dir="${file%%/pipeline_info/*}"
+    else
+        top_dir=""
+        dir=$(dirname "$file")
+        while [[ "$dir" != "." && "$dir" != "/" ]]; do
+            if [[ -d "$dir/pipeline_info" ]]; then
+                top_dir="$dir"
+                break
+            fi
+            dir=$(dirname "$dir")
+        done
+    fi
+
+    if [[ -n "$top_dir" ]]; then
+        echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file"
+        status=1
+        case "$seen_dirs" in
+            *"|$top_dir|"*) ;;
+            *)
+                echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area."
+                seen_dirs="$seen_dirs|$top_dir|"
+                ;;
+        esac
+    fi
+done < <(git diff --cached --name-only)
+
+exit "$status"
diff --git a/.nf-core.yml b/.nf-core.yml
index 4ee9291..ba11b10 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,6 +2,7 @@ lint:
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
+    - .github/workflows/linting_comment.yml
   files_unchanged:
     - .gitattributes
     - .gitignore
@@ -9,7 +10,9 @@ lint:
     - assets/nf-core-spatialvi_logo_light.png
     - docs/images/nf-core-spatialvi_logo_light.png
     - docs/images/nf-core-spatialvi_logo_dark.png
-nf_core_version: 4.0.3
+    - .github/workflows/branch.yml
+    - .github/workflows/linting.yml
+nf_core_version: 4.1.0
 repository_type: pipeline
 template:
   author: Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f51e1a2..e9503db 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -25,9 +25,26 @@ repos:
               subworkflows/(?!local/).*|
               .*\.snap$
           )$
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              .*\.snap$|
+              lib/nfcore_external_java_deps.jar$|
+              docs/.*\.(svg|pdf)$|
+              assets/.*$
+          )$
+      - id: check-merge-conflict
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit
     rev: v0.3.0
     hooks:
       - id: nextflow-lint
         files: '\.nf$|nextflow\.config$'
         args: ["-output", "json"]
+  - repo: local
+    hooks:
+      - id: block-pipeline-outdir
+        name: Prevent committing output from pipeline test runs to the pipeline code itself
+        entry: ./.hooks/block_pipeline_outdir.sh
+        language: script
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7af7cd7..485426e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v1.0dev - [unreleased<!-- TODO nf-core: replace with date on release -->]
 
 Initial release of nf-core/spatialvi, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/README.md b/README.md
index b0ae453..214403e 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/conf/base.config b/conf/base.config
index 11cae92..bf3b861 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -49,6 +49,9 @@ process {
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
+    withLabel:process_low_memory {
+        memory = { 1.GB * task.attempt }
+    }
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
index d3ee1b4..df04a4b 100644
--- a/conf/containers_conda_lock_files_amd64.config
+++ b/conf/containers_conda_lock_files_amd64.config
@@ -1,2 +1,2 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
index 2b90ac4..7ed29f3 100644
--- a/conf/containers_conda_lock_files_arm64.config
+++ b/conf/containers_conda_lock_files_arm64.config
@@ -1,2 +1,2 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
index 65f1814..a66e3d1 100644
--- a/conf/containers_docker_amd64.config
+++ b/conf/containers_docker_amd64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
index 6c845ba..215f686 100644
--- a/conf/containers_docker_arm64.config
+++ b/conf/containers_docker_arm64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
index 838f248..2fb11a3 100644
--- a/conf/containers_singularity_https_amd64.config
+++ b/conf/containers_singularity_https_amd64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
index 090173b..5fa5b4f 100644
--- a/conf/containers_singularity_https_arm64.config
+++ b/conf/containers_singularity_https_arm64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
index 773f369..b334375 100644
--- a/conf/containers_singularity_oras_amd64.config
+++ b/conf/containers_singularity_oras_amd64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
index 798cc63..661c656 100644
--- a/conf/containers_singularity_oras_arm64.config
+++ b/conf/containers_singularity_oras_arm64.config
@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }
diff --git a/conf/modules.config b/conf/modules.config
index d203d2b..d4e90be 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -26,8 +26,7 @@ process {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
index 1026c8b..c9ac4d2 100644
--- a/docs/CONTRIBUTING.md
+++ b/docs/CONTRIBUTING.md
@@ -40,12 +40,12 @@ The nf-core stance on the use of AI and LLMs is that humans are still ultimately
 
 If you’re using AI tools, try to stick by these guidelines:
 
-- Keep PRs as small and focussed as possible
+- Keep PRs as small and focused as possible
 - Avoid any unnecessary changes, such as moving or refactoring code (unless that is the explicit intention of the PR)
 - Review all generated code yourself before opening a PR, and ensure that you understand it
 - Engage with the community review process and expect to make revisions
 
-For more detail, see the the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
+For more detail, see the [blog post](https://nf-co.re/blog/2026/statement-on-ai) for a statement from the nf-core/core team.
 
 ### Getting help
 
@@ -128,7 +128,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s
 - [ ] Perform local tests to validate that the new code works as expected.
   - [ ] If applicable, add a new test in the `tests` directory.
 - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate.
-- [ ] [Lint](lint) the code with nf-core/tools.
+- [ ] [Lint](#lint-tests) the code with nf-core/tools.
 - [ ] Update any diagrams or pipeline images as necessary.
 - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order.
 - [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module.
@@ -166,7 +166,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across
 nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config).
 These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements.
 
-Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
+Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)).
 
 #### Nextflow version bumping
 
diff --git a/docs/output.md b/docs/output.md
index e456810..d16a45e 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -58,4 +58,4 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 </details>
 
-[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
+[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.
diff --git a/docs/usage.md b/docs/usage.md
index 5143d00..c926c44 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -152,7 +152,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
 - `wave`
-  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index c58ba08..085e22a 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215",
+                        "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
                         "installed_by": ["modules"]
                     }
                 }
@@ -21,7 +21,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -31,7 +31,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
new file mode 100644
index 0000000..2a91c22
--- /dev/null
+++ b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
@@ -0,0 +1,1526 @@
+
+version: 6
+environments:
+default:
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+- url: https://conda.anaconda.org/bioconda/
+- url: https://conda.anaconda.org/bioconda/
+options:
+pypi-prerelease-mode: if-necessary-or-explicit
+packages:
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diff --git a/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
new file mode 100644
index 0000000..3d5b93d
--- /dev/null
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+- libsqlite 3.53.1 h022381a_0
+- libzlib >=1.3.2,<2.0a0
+- ncurses >=6.6,<7.0a0
+- readline >=8.3,<9.0a0
+license: blessing
+size: 209964
+timestamp: 1777986493350
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda
+sha256: c1da41c79262b27efa168407cfecc47b20270e5fc071a8307f95a2c85fb94170
+md5: 55bf7b559202236157b14323b40f19e6
+depends:
+- libgcc >=14
+- libstdcxx >=14
+- python >=3.14,<3.15.0a0
+- python_abi 3.14.* *_cp314
+- regex >=2022.1.18
+- requests >=2.26.0
+constrains:
+- __glibc >=2.17
+license: MIT
+license_family: MIT
+size: 914402
+timestamp: 1764030357702
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.13-noxft_h0dc03b3_103.conda
+sha256: e25c314b52764219f842b41aea2c98a059f06437392268f09b03561e4f6e5309
+md5: 7fc6affb9b01e567d2ef1d05b84aa6ed
+depends:
+- libgcc >=14
+- libzlib >=1.3.1,<2.0a0
+constrains:
+- xorg-libx11 >=1.8.12,<2.0a0
+license: TCL
+license_family: BSD
+size: 3368666
+timestamp: 1769464148928
+- conda: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda
+sha256: 9ef8e47cf00e4d6dcc114eb32a1504cc18206300572ef14d76634ba29dfe1eb6
+md5: e5ce43272193b38c2e9037446c1d9206
+depends:
+- python >=3.10
+- __unix
+- python
+license: MPL-2.0 and MIT
+size: 94132
+timestamp: 1770153424136
+- conda: https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.2-pyhcf101f3_0.conda
+sha256: 59d7851d32fddb5b510272e6557aa982edeb927d349648dac27f5bf01d18bb26
+md5: 4460f039b7dedf15f7df086446ca75ae
+depends:
+- typing_extensions >=4.14.0
+- python >=3.10
+- importlib-metadata >=3.6
+- python
+constrains:
+- pytest >=7
+license: MIT
+license_family: MIT
+size: 38297
+timestamp: 1778779291237
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.15.0-h396c80c_0.conda
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+md5: edd329d7d3a4ab45dcf905899a7a6115
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+- typing_extensions ==4.15.0 pyhcf101f3_0
+license: PSF-2.0
+license_family: PSF
+size: 91383
+timestamp: 1756220668932
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhcf101f3_2.conda
+sha256: 8b90d2f19f9458b8c58a55e1fcdc1d90c1603a847a47654d8a454549413ba60a
+md5: 53f5409c5cfd6c5a66417d68e3f0a864
+depends:
+- python >=3.10
+- typing_extensions >=4.12.0
+- python
+license: MIT
+license_family: MIT
+size: 20935
+timestamp: 1777105465795
+- conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda
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+depends:
+- python >=3.10
+- python
+license: PSF-2.0
+license_family: PSF
+size: 51692
+timestamp: 1756220668932
+- conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
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+license: LicenseRef-Public-Domain
+size: 119135
+timestamp: 1767016325805
+- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.7.0-pyhd8ed1ab_0.conda
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+- backports.zstd >=1.0.0
+- brotli-python >=1.2.0
+- h2 >=4,<5
+- pysocks >=1.5.6,<2.0,!=1.5.7
+- python >=3.10
+license: MIT
+license_family: MIT
+size: 103560
+timestamp: 1778188657149
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxau-1.0.12-he30d5cf_1.conda
+sha256: e9f6e931feeb2f40e1fdbafe41d3b665f1ab6cb39c5880a1fcf9f79a3f3c84a5
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+depends:
+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 16317
+timestamp: 1762977521691
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxdmcp-1.1.5-he30d5cf_1.conda
+sha256: 128d72f36bcc8d2b4cdbec07507542e437c7d67f677b7d77b71ed9eeac7d6df1
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+- libgcc >=14
+license: MIT
+license_family: MIT
+size: 21039
+timestamp: 1762979038025
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda
+sha256: 66265e943f32ce02396ad214e27cb35f5b0490b3bd4f064446390f9d67fa5d88
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+- libgcc >=14
+license: MIT
+license_family: MIT
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+timestamp: 1753484092643
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-4.1.0-pyhcf101f3_0.conda
+sha256: 210bd31c22bb88f5e2a167df24c95bb5f152b2ada7502f9b8c49d1f5366db423
+md5: ba3dcdc8584155c97c648ae9c044b7a3
+depends:
+- python >=3.10
+- python
+license: MIT
+license_family: MIT
+size: 24190
+timestamp: 1779159948016
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-ng-2.3.3-ha7cb516_1.conda
+sha256: 638a3a41a4fbfed52d3c60c8ef5a3693b3f12a5b1a3f58fa29f5698d0a0702e2
+md5: f731af71c723065d91b4c01bb822641b
+depends:
+- libgcc >=14
+- libstdcxx >=14
+license: Zlib
+license_family: Other
+size: 121046
+timestamp: 1770167944449
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda
+sha256: 569990cf12e46f9df540275146da567d9c618c1e9c7a0bc9d9cfefadaed20b75
+md5: c3655f82dcea2aa179b291e7099c1fcc
+depends:
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+license: BSD-3-Clause
+license_family: BSD
+size: 614429
+timestamp: 1764777145593
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 37e7612..7a970e2 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.34
+  - bioconda::multiqc=1.35
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index e80e8cd..c4bc715 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -4,8 +4,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data'
-        : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}"
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data'
+        : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}"
 
     input:
     tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names)
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 2facc62..27ce18d 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -110,24 +110,24 @@ maintainers:
 containers:
   conda:
     linux/amd64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt
     linux/arm64:
-      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt
+      lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt
   docker:
     linux/amd64:
-      name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6
-      build_id: bd-db7c73dae76bc9e6_1
-      scan_id: sc-66fc7138dbf1cf48_1
+      name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc
+      build_id: bd-c17fb751507e9dfc_1
+      scan_id: sc-3b1b3932f9846892_1
     linux/arm64:
-      name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136
-      build_id: bd-d167b8012595a136_1
-      scan_id: sc-ac701dfa631a2af9_1
+      name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5
+      build_id: bd-5c84a5000a226ab5_1
+      scan_id: sc-0d39df41e9737bbd_1
   singularity:
     linux/amd64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0
-      build_id: bd-4fc8657c816047c0_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2
+      build_id: bd-c680f2aea25ccec2_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data
     linux/arm64:
-      name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726
-      build_id: bd-7fbd82d945c06726_1
-      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data
+      name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81
+      build_id: bd-c0468833d65b2f81_1
+      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7c2f370..4489921 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -81,7 +81,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -175,7 +175,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -221,7 +221,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -314,7 +314,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
@@ -408,7 +408,7 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.34"
+                        "1.35"
                     ]
                 ]
             }
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 78bd815..c739ded 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2026-07-24T12:36:21+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialvi_logo_dark.png\">\n    <img alt=\"nf-core/spatialvi\" src=\"docs/images/nf-core-spatialvi_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialvi)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialvi/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialvi/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/spatialvi/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/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)\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/spatialvi)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialvi-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialvi)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/spatialvi** 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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-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/spatialvi \\\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/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/spatialvi/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/spatialvi/output).\n\n## Credits\n\nnf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialvi` channel](https://nfcore.slack.com/channels/spatialvi) (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/spatialvi 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",
+            "datePublished": "2026-09-01T13:07:09+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialvi_logo_dark.png\">\n    <img alt=\"nf-core/spatialvi\" src=\"docs/images/nf-core-spatialvi_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialvi)\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialvi/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialvi/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialvi/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/spatialvi/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/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\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/spatialvi)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialvi-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialvi)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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/spatialvi** 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/community/brand/workflow-schematics#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-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/spatialvi \\\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/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialvi/usage) and the [parameter documentation](https://nf-co.re/spatialvi/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/spatialvi/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/spatialvi/output).\n\n## Credits\n\nnf-core/spatialvi was originally written by Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava.\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](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialvi` channel](https://nfcore.slack.com/channels/spatialvi) (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/spatialvi 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"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#943c68f0-8198-411c-bc67-2c4185d0bd3e"
+                    "@id": "#57fdd2fd-3be6-4e39-ae0f-a356abbf6c58"
                 }
             ],
             "name": "nf-core/spatialvi"
@@ -136,11 +136,11 @@
                     "@id": "https://orcid.org/0000-0002-3298-2358"
                 },
                 {
-                    "@id": "#ef2d6ff5-4891-454d-b799-6123121c466b"
+                    "@id": "#b0ed9c19-92df-4349-b30d-a56544f4b4ab"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2026-07-24T12:36:21Z",
+            "dateModified": "2026-09-01T13:07:09Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -181,11 +181,11 @@
             "version": "!>=25.10.4"
         },
         {
-            "@id": "#943c68f0-8198-411c-bc67-2c4185d0bd3e",
+            "@id": "#57fdd2fd-3be6-4e39-ae0f-a356abbf6c58",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#1ebb83ae-7830-4731-9382-62769ca97ac1"
+                    "@id": "#fb38355d-9b73-4279-b664-2b44e3cb8c1c"
                 }
             ],
             "mainEntity": {
@@ -194,7 +194,7 @@
             "name": "Test suite for nf-core/spatialvi"
         },
         {
-            "@id": "#1ebb83ae-7830-4731-9382-62769ca97ac1",
+            "@id": "#fb38355d-9b73-4279-b664-2b44e3cb8c1c",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/spatialvi",
             "resource": "repos/nf-core/spatialvi/actions/workflows/nf-test.yml",
@@ -346,7 +346,7 @@
             "name": "Jeffrey Chuang"
         },
         {
-            "@id": "#ef2d6ff5-4891-454d-b799-6123121c466b",
+            "@id": "#b0ed9c19-92df-4349-b30d-a56544f4b4ab",
             "@type": "Person",
             "name": "Anuj Srivastava"
         }
diff --git a/subworkflows/local/utils_nfcore_spatialvi_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialvi_pipeline/main.nf
index 3e50db7..c9f2e43 100644
--- a/subworkflows/local/utils_nfcore_spatialvi_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_spatialvi_pipeline/main.nf
@@ -88,7 +88,8 @@ workflow PIPELINE_INITIALISATION {
         show_hidden,
         before_text,
         after_text,
-        command
+        command,
+        false
     )
 
     //
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
index 1df8b76..9ff0681 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf
+++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf
@@ -22,6 +22,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     before_text         // string:   text to show before the help message and parameters summary
     after_text          // string:   text to show after the help message and parameters summary
     command             // string:   an example command of the pipeline
+    cli_typecast        // boolean:  whether to perform typecasting of CLI parameters. Set this to `null` to use the default behaviour
 
     main:
 
@@ -34,11 +35,11 @@ workflow UTILS_NFSCHEMA_PLUGIN {
             fullHelp: help_full,
         ]
         if(parameters_schema) {
-            help_options << [parametersSchema: parameters_schema]
+            help_options << [parameters_schema: parameters_schema]
         }
         log.info paramsHelp(
             help_options,
-            (params.help instanceof String && params.help != "true") ? params.help : "",
+            (help instanceof String && help != "true") ? help : "",
         )
         exit 0
     }
@@ -50,7 +51,7 @@ workflow UTILS_NFSCHEMA_PLUGIN {
 
     summary_options = [:]
     if(parameters_schema) {
-        summary_options << [parametersSchema: parameters_schema]
+        summary_options << [parameters_schema: parameters_schema]
     }
     log.info before_text
     log.info paramsSummaryLog(summary_options, input_workflow)
@@ -63,7 +64,10 @@ workflow UTILS_NFSCHEMA_PLUGIN {
     if(validate_params) {
         validateOptions = [:]
         if(parameters_schema) {
-            validateOptions << [parametersSchema: parameters_schema]
+            validateOptions << [parameters_schema: parameters_schema]
+        }
+        if(cli_typecast != null) {
+            validateOptions << [cast_cli_params: cli_typecast]
         }
         validateParameters(validateOptions)
     }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
index f7d9f02..1d8c75a 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
+++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml
@@ -25,6 +25,30 @@ input:
         option. When this input is empty it will automatically use the configured schema or
         "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way
         for meta pipelines.
+  - help:
+      type: boolean, string
+      description: |
+        Show the help message and exit. When a parameter name is given, show the help message for that parameter instead of the general help message.
+  - help_full:
+      type: boolean
+      description: Show the full help message and exit.
+  - show_hidden:
+      type: boolean
+      description: Show hidden parameters in the help message.
+  - before_text:
+      type: string
+      description: Text to show before the parameters summary and help message.
+  - after_text:
+      type: string
+      description: Text to show after the parameters summary and help message.
+  - command:
+      type: string
+      description: An example command to run the pipeline, to show in the help message and the summary.
+  - cli_typecast:
+      type: boolean
+      description: |
+        Whether to apply typecasting to the parameters given via the CLI before validation.
+        Set this to `null` to use the default behavior.
 output:
   - dummy_emit:
       type: boolean
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 c977917..1fd1eac 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
@@ -31,6 +31,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -63,6 +64,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -95,6 +97,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -127,6 +130,7 @@ nextflow_workflow {
                 input[6] = ""
                 input[7] = ""
                 input[8] = ""
+                input[9] = null
                 """
             }
         }
@@ -160,6 +164,7 @@ nextflow_workflow {
                 input[6] = "Before"
                 input[7] = "After"
                 input[8] = "nextflow run test/test"
+                input[9] = null
                 """
             }
         }
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index f6537cc..fd71cb8 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id "nf-schema@2.6.1"
+    id "nf-schema@2.7.2"
 }
 
 validation {
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 1565e69..f4631ba 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -8,7 +8,8 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/spatialvi/'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/spatialvi/'
 }
 
-aws.client.anonymous = true // fixes S3 access issues on self-hosted runners
+// Fixes S3 access issues on self-hosted runners
+aws.client.anonymous = true

From a533629a0a88c41e2be69c30d5b74e446357df45 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Tue, 1 Sep 2026 17:54:28 +0200
Subject: [PATCH 3/3] Fix bug with `nextflow config -o json` closures

Fix bug in how publishDir was used in `conf/modules.config` in cases
with lists of maps, which made `nextflow config -o json` (used in
linting) eagerly evaluate _e.g._ `${meta.id}` inside the lists of maps;
use conditional `saveAs` instead.
---
 conf/modules.config | 60 ++++++++++++++++++++-------------------------
 1 file changed, 26 insertions(+), 34 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index a002fec..400e91c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -75,23 +75,19 @@ process {
         ext.args = { "--metadata subtitle:'Sample: ${meta.id}'" }
         container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
-            [
-                path: { "${params.outdir}/${meta.id}/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "*{.html,.qmd,_extensions}"
-            ],
-            [
-                path: { "${params.outdir}/${meta.id}/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "params.yml",
-                saveAs: { "${notebook.baseName}.yml" }
-            ],
-            [
-                path: { "${params.outdir}/${meta.id}/plots" },
-                mode: params.publish_dir_mode,
-                pattern: "artifacts/*.png",
-                saveAs: { filename -> filename.split('/')[1] }
-            ]
+            path: { "${params.outdir}/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename ==~ /.*\.(html|qmd)$/ || filename.endsWith('_extensions')) {
+                    "reports/${filename}"
+                } else if (filename == 'params.yml') {
+                    "reports/${notebook.baseName}.yml"
+                } else if (filename.startsWith('artifacts/') && filename.endsWith('.png')) {
+                    "plots/${filename.split('/')[1]}"
+                } else {
+                    null
+                }
+            }
         ]
     }
 
@@ -124,23 +120,19 @@ process {
         ext.prefix = { "${notebook.baseName}" }
         container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
-            [
-                path: { "${params.outdir}/integration/reports"},
-                mode: params.publish_dir_mode,
-                pattern: "*{.html,.qmd,_extensions}"
-            ],
-            [
-                path: { "${params.outdir}/integration/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "params.yml",
-                saveAs: { "${notebook.baseName}.yml" }
-            ],
-            [
-                path: { "${params.outdir}/integration/plots" },
-                mode: params.publish_dir_mode,
-                pattern: "artifacts/*.png",
-                saveAs: { filename -> filename.split('/')[1] }
-            ]
+            path: { "${params.outdir}/integration" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename ==~ /.*\.(html|qmd)$/ || filename.endsWith('_extensions')) {
+                    "reports/${filename}"
+                } else if (filename == 'params.yml') {
+                    "reports/${notebook.baseName}.yml"
+                } else if (filename.startsWith('artifacts/') && filename.endsWith('.png')) {
+                    "plots/${filename.split('/')[1]}"
+                } else {
+                    null
+                }
+            }
         ]
     }