From 5fc6b58dbe1a2ac38a2e0e4b96136cdb79757ecd Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 3 Jun 2025 11:02:03 +0000
Subject: [PATCH 1/8] Template update for nf-core/tools version 3.3.1

---
 .editorconfig                                 |  37 -----
 .github/CONTRIBUTING.md                       |   2 +-
 .github/actions/get-shards/action.yml         |  69 +++++++++
 .github/actions/nf-test/action.yml            | 113 ++++++++++++++
 .github/workflows/awsfulltest.yml             |   4 +-
 .github/workflows/awstest.yml                 |   2 +-
 .github/workflows/ci.yml                      |  88 -----------
 .github/workflows/clean-up.yml                |   2 +-
 .github/workflows/download_pipeline.yml       |  20 +--
 .../{fix-linting.yml => fix_linting.yml}      |   4 +-
 .github/workflows/linting.yml                 |  15 +-
 .github/workflows/linting_comment.yml         |   4 +-
 .github/workflows/nf-test.yml                 | 142 ++++++++++++++++++
 .github/workflows/release-announcements.yml   |   2 +-
 ...mment.yml => template-version-comment.yml} |   2 +-
 .nf-core.yml                                  |  11 +-
 .pre-commit-config.yaml                       |  26 +++-
 .prettierrc.yml                               |   5 +
 README.md                                     |   7 +-
 conf/base.config                              |   5 +-
 nextflow.config                               |  17 ++-
 nf-test.config                                |  24 +++
 ro-crate-metadata.json                        |  16 +-
 .../utils_nfcore_spatialxe_pipeline/main.nf   |   1 -
 tests/.nftignore                              |  10 ++
 tests/default.nf.test                         |  35 +++++
 tests/nextflow.config                         |  12 ++
 27 files changed, 496 insertions(+), 179 deletions(-)
 delete mode 100644 .editorconfig
 create mode 100644 .github/actions/get-shards/action.yml
 create mode 100644 .github/actions/nf-test/action.yml
 delete mode 100644 .github/workflows/ci.yml
 rename .github/workflows/{fix-linting.yml => fix_linting.yml} (96%)
 create mode 100644 .github/workflows/nf-test.yml
 rename .github/workflows/{template_version_comment.yml => template-version-comment.yml} (95%)
 create mode 100644 nf-test.config
 create mode 100644 tests/.nftignore
 create mode 100644 tests/default.nf.test
 create mode 100644 tests/nextflow.config

diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 6d9b74cc..00000000
--- a/.editorconfig
+++ /dev/null
@@ -1,37 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
-
-# ignore ro-crate metadata files
-[**/ro-crate-metadata.json]
-insert_final_newline = unset
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index acdd7f34..6264525d 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -78,7 +78,7 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+8. If applicable, add a new test in the `tests` directory.
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 00000000..34085279
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,69 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: ${{ env.NFT_VER }}
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --profile +docker \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --dry-run \
+          --ci \
+          --changed-since HEAD^) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 00000000..243e7823
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,113 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: false
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      with:
+        python-version: "3.13"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+        install-pdiff: true
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: contains(inputs.profile, 'conda')
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        NFT_DIFF: ${{ env.NFT_DIFF }}
+        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+      run: |
+        nf-test test \
+          --profile=+${{ inputs.profile }} \
+          $(if [ -n "${{ inputs.tags }}" ]; then echo "--tag ${{ inputs.tags }}"; fi) \
+          --ci \
+          --changed-since HEAD^ \
+          --verbose \
+          --tap=test.tap \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 1d87e5d5..5449e8c1 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == 'nf-core/spatialxe' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/spatialxe' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 042b25d6..24c7ddf9 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 93cf0ac5..00000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,88 +0,0 @@
-name: nf-core CI
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on:
-  push:
-    branches:
-      - dev
-  pull_request:
-  release:
-    types: [published]
-  workflow_dispatch:
-
-env:
-  NXF_ANSI_LOG: false
-  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
-  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
-
-concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
-  cancel-in-progress: true
-
-jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/spatialxe') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        test_name:
-          - "test"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        # Exclude conda and singularity on dev
-        exclude:
-          - isMaster: false
-            profile: "conda"
-          - isMaster: false
-            profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
index 0b6b1f27..ac030fd5 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@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
+      - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index ab06316e..999bcc38 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -12,14 +12,6 @@ on:
         required: true
         default: "dev"
   pull_request:
-    types:
-      - opened
-      - edited
-      - synchronize
-    branches:
-      - main
-      - master
-  pull_request_target:
     branches:
       - main
       - master
@@ -52,9 +44,9 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: Setup Apptainer
@@ -120,6 +112,7 @@ jobs:
           echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
+        id: count_comparison
         run: |
           if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
             initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
@@ -132,3 +125,10 @@ jobs:
           else
             echo "The pipeline can be downloaded successfully!"
           fi
+
+      - name: Upload Nextflow logfile for debugging purposes
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: nextflow_logfile.txt
+          path: .nextflow.log*
+          include-hidden-files: true
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix_linting.yml
similarity index 96%
rename from .github/workflows/fix-linting.yml
rename to .github/workflows/fix_linting.yml
index 8dade217..db468f92 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix_linting.yml
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index dbd52d5a..f2d7d1dd 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -3,9 +3,6 @@ name: nf-core linting
 # It runs the `nf-core pipelines lint` and markdown lint tests to ensure
 # that the code meets the nf-core guidelines.
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -17,9 +14,9 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -36,13 +33,13 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.1.0
+        uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -74,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 95b6b6af..7e8050fb 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
+        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 00000000..f03aea0c
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,142 @@
+name: Run nf-test
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test-changes
+      - runner=4cpu-linux-x64
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 7
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    runs-on: # use self-hosted runners
+      - runs-on=$-nf-test
+      - runner=4cpu-linux-x64
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMain:
+          - ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMain: false
+            profile: "conda"
+          - isMain: false
+            profile: "singularity"
+        NXF_VER:
+          - "24.04.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+  confirm-pass:
+    needs: [nf-test]
+    if: always()
+    runs-on: # use self-hosted runners
+      - runs-on=$-confirm-pass
+      - runner=2cpu-linux-x64
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 76a9e67e..4abaf484 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
+      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template-version-comment.yml
similarity index 95%
rename from .github/workflows/template_version_comment.yml
rename to .github/workflows/template-version-comment.yml
index 537529bc..beb5c77f 100644
--- a/.github/workflows/template_version_comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -14,7 +14,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: nichmor/minimal-read-yaml@v0.0.2
+        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
diff --git a/.nf-core.yml b/.nf-core.yml
index 3ce56233..bade232c 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,4 +1,13 @@
-nf_core_version: 3.2.1
+lint:
+  files_exist:
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+  files_unchanged:
+    - .gitignore
+    - assets/nf-core-spatialxe_logo_light.png
+    - docs/images/nf-core-spatialxe_logo_dark.png
+    - docs/images/nf-core-spatialxe_logo_light.png
+nf_core_version: 3.3.1
 repository_type: pipeline
 template:
   author: Florian Heyl
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1dec8650..9d0b248d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,10 +4,24 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+          - prettier@3.5.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
diff --git a/.prettierrc.yml b/.prettierrc.yml
index c81f9a76..07dbd8bb 100644
--- a/.prettierrc.yml
+++ b/.prettierrc.yml
@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2
diff --git a/README.md b/README.md
index 789d6b97..bfb1a29a 100644
--- a/README.md
+++ b/README.md
@@ -9,13 +9,14 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on 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/spatialxe)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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)
 
 ## Introduction
 
@@ -28,7 +29,7 @@
 -->
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
 <!-- 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/))
 
 ## Usage
diff --git a/conf/base.config b/conf/base.config
index 83786f2d..d656b80a 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
@@ -59,4 +59,7 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+    }
 }
diff --git a/nextflow.config b/nextflow.config
index f84f7623..f0109a71 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -160,16 +160,25 @@ profiles {
             ]
         }
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+    }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Load nf-core custom profiles from different Institutions
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions
+
+// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
+// Load nf-core/spatialxe custom profiles from different institutions.
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+
 
 // Load nf-core/spatialxe custom profiles from different institutions.
 // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/spatialxe.config" : "/dev/null"
+// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/spatialxe.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -249,7 +258,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
new file mode 100644
index 00000000..889df760
--- /dev/null
+++ b/nf-test.config
@@ -0,0 +1,24 @@
+config {
+    // location for all nf-test tests
+    testsDir "."
+
+    // nf-test directory including temporary files for each test
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "tests/nextflow.config"
+
+    // ignore tests coming from the nf-core/modules repo
+    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+
+    // run all test with defined profile(s) from the main nextflow.config
+    profile "test"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore'
+
+    // load the necessary plugins
+    plugins {
+        load "nft-utils@0.0.3"
+    }
+}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index e98f8c56..d23c6938 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-04-30T12:28:31+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/spatialxe** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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": "2025-06-03T11:01:58+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** 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/guidelines/graphic_design/workflow_diagrams#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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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": "#28a1ccb5-5f41-4bf5-89a5-41054b85557d"
+                    "@id": "#05227869-464b-481c-b6f5-9d03620ece88"
                 }
             ],
             "name": "nf-core/spatialxe"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-04-30T12:28:31Z",
+            "dateModified": "2025-06-03T11:01:58Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow"],
             "license": ["MIT"],
@@ -150,11 +150,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#28a1ccb5-5f41-4bf5-89a5-41054b85557d",
+            "@id": "#05227869-464b-481c-b6f5-9d03620ece88",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#d4948f75-e334-4285-bd4f-003ee9ce7891"
+                    "@id": "#33cd4a92-cf89-45d4-a66c-79db7722e6f3"
                 }
             ],
             "mainEntity": {
@@ -163,10 +163,10 @@
             "name": "Test suite for nf-core/spatialxe"
         },
         {
-            "@id": "#d4948f75-e334-4285-bd4f-003ee9ce7891",
+            "@id": "#33cd4a92-cf89-45d4-a66c-79db7722e6f3",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/spatialxe",
-            "resource": "repos/nf-core/spatialxe/actions/workflows/ci.yml",
+            "resource": "repos/nf-core/spatialxe/actions/workflows/nf-test.yml",
             "runsOn": {
                 "@id": "https://w3id.org/ro/terms/test#GithubService"
             },
diff --git a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
index ff0ad5d3..a6fa922c 100644
--- a/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_spatialxe_pipeline/main.nf
@@ -261,4 +261,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..c10bc1f1
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,10 @@
+.DS_Store
+multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/multiqc.log
+multiqc/multiqc_data/multiqc_data.json
+multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/multiqc_report.html
+fastqc/*_fastqc.{html,zip}
+pipeline_info/*.{html,json,txt,yml}
diff --git a/tests/default.nf.test b/tests/default.nf.test
new file mode 100644
index 00000000..84b58fa7
--- /dev/null
+++ b/tests/default.nf.test
@@ -0,0 +1,35 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("-profile test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_spatialxe_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 00000000..580e3643
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1,12 @@
+/*
+========================================================================================
+    Nextflow config file for running nf-test tests
+========================================================================================
+*/
+
+// TODO nf-core: Specify any additional parameters here
+// Or any resources requirements
+params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/spatialxe'
+
+aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From 791aa1cee6405c738f7349fd147179d5bc4b3ffc Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 8 Jul 2025 11:39:11 +0000
Subject: [PATCH 2/8] Template update for nf-core/tools version 3.3.2

---
 .github/actions/nf-test/action.yml            |   4 -
 .github/workflows/linting.yml                 |   2 +-
 .github/workflows/linting_comment.yml         |   2 +-
 .github/workflows/nf-test.yml                 |  45 +++----
 .github/workflows/release-announcements.yml   |   2 +-
 .nf-core.yml                                  |   2 +-
 .pre-commit-config.yaml                       |   2 +-
 README.md                                     |   6 +-
 assets/schema_input.json                      |   4 +-
 conf/base.config                              |   1 +
 modules.json                                  |   4 +-
 modules/nf-core/fastqc/environment.yml        |   2 +
 modules/nf-core/fastqc/main.nf                |   2 +-
 modules/nf-core/fastqc/meta.yml               |  23 ++--
 modules/nf-core/multiqc/environment.yml       |   4 +-
 modules/nf-core/multiqc/main.nf               |   4 +-
 modules/nf-core/multiqc/meta.yml              | 110 ++++++++++--------
 .../nf-core/multiqc/tests/main.nf.test.snap   |  18 +--
 nextflow.config                               |   5 +-
 nf-test.config                                |   2 +-
 ro-crate-metadata.json                        |  16 +--
 .../tests/nextflow.config                     |   2 +-
 tests/.nftignore                              |   1 +
 tests/nextflow.config                         |   6 +-
 24 files changed, 146 insertions(+), 123 deletions(-)

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 243e7823..bf44d961 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index f2d7d1dd..8b0f88c3 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index 7e8050fb..d43797d9 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f03aea0c..e7b58449 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,12 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -35,7 +28,7 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -69,7 +62,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
     strategy:
       fail-fast: false
@@ -85,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -97,23 +90,39 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -132,11 +141,3 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index 4abaf484..0f732495 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
diff --git a/.nf-core.yml b/.nf-core.yml
index bade232c..f84e1b7a 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,7 +7,7 @@ lint:
     - assets/nf-core-spatialxe_logo_light.png
     - docs/images/nf-core-spatialxe_logo_dark.png
     - docs/images/nf-core-spatialxe_logo_light.png
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Florian Heyl
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9d0b248d..bb41beec 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
diff --git a/README.md b/README.md
index bfb1a29a..76ef8a96 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml)
+[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/assets/schema_input.json b/assets/schema_input.json
index 11024035..7435ad64 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -17,14 +17,14 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             }
         },
diff --git a/conf/base.config b/conf/base.config
index d656b80a..fcfae939 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -61,5 +61,6 @@ process {
     }
     withLabel: process_gpu {
         ext.use_gpu = { workflow.profile.contains('gpu') }
+        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
 }
diff --git a/modules.json b/modules.json
index 4d983cac..74afbbf0 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 691d4c76..f9f54ee9 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..23e16634 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,7 @@ process FASTQC {
     // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
     // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
     // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null
+    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 2b2e62b8..c8d9d025 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -29,9 +29,10 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
+        ontologies: []
 output:
-  - html:
-      - meta:
+  html:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -40,8 +41,9 @@ output:
           type: file
           description: FastQC report
           pattern: "*_{fastqc.html}"
-  - zip:
-      - meta:
+          ontologies: []
+  zip:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -50,11 +52,14 @@ output:
           type: file
           description: FastQC report archive
           pattern: "*_{fastqc.zip}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
   - "@grst"
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index a27122ce..812fc4c5 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -1,5 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.27
+  - bioconda::multiqc=1.29
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 58d9313c..0ac3c369 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.27--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.29--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index b16c1879..ce30eb73 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -15,57 +15,71 @@ tools:
       licence: ["GPL-3.0-or-later"]
       identifier: biotools:multiqc
 input:
-  - - multiqc_files:
-        type: file
-        description: |
-          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - - multiqc_config:
-        type: file
-        description: Optional config yml for MultiQC
-        pattern: "*.{yml,yaml}"
-  - - extra_multiqc_config:
-        type: file
-        description: Second optional config yml for MultiQC. Will override common sections
-          in multiqc_config.
-        pattern: "*.{yml,yaml}"
-  - - multiqc_logo:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+      ontologies: []
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections
+        in multiqc_config.
+      pattern: "*.{yml,yaml}"
+      ontologies:
+        - edam: http://edamontology.org/format_3750 # YAML
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+      ontologies: []
+  - replace_names:
+      type: file
+      description: |
+        Optional two-column sample renaming file. First column a set of
+        patterns, second column a set of corresponding replacements. Passed via
+        MultiQC's `--replace-names` option.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+  - sample_names:
+      type: file
+      description: |
+        Optional TSV file with headers, passed to the MultiQC --sample_names
+        argument.
+      pattern: "*.{tsv}"
+      ontologies:
+        - edam: http://edamontology.org/format_3475 # TSV
+output:
+  report:
+    - "*multiqc_report.html":
         type: file
-        description: Optional logo file for MultiQC
-        pattern: "*.{png}"
-  - - replace_names:
+        description: MultiQC report file
+        pattern: "multiqc_report.html"
+        ontologies: []
+  data:
+    - "*_data":
+        type: directory
+        description: MultiQC data dir
+        pattern: "multiqc_data"
+  plots:
+    - "*_plots":
         type: file
-        description: |
-          Optional two-column sample renaming file. First column a set of
-          patterns, second column a set of corresponding replacements. Passed via
-          MultiQC's `--replace-names` option.
-        pattern: "*.{tsv}"
-  - - sample_names:
+        description: Plots created by MultiQC
+        pattern: "*_data"
+        ontologies: []
+  versions:
+    - versions.yml:
         type: file
-        description: |
-          Optional TSV file with headers, passed to the MultiQC --sample_names
-          argument.
-        pattern: "*.{tsv}"
-output:
-  - report:
-      - "*multiqc_report.html":
-          type: file
-          description: MultiQC report file
-          pattern: "multiqc_report.html"
-  - data:
-      - "*_data":
-          type: directory
-          description: MultiQC data dir
-          pattern: "multiqc_data"
-  - plots:
-      - "*_plots":
-          type: file
-          description: Plots created by MultiQC
-          pattern: "*_data"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@bunop"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 7b7c1322..88e90571 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:29:57.631982377"
+        "timestamp": "2025-05-22T11:50:41.182332996"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:34.743726958"
+        "timestamp": "2025-05-22T11:51:22.448739369"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+                "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-01-27T09:30:21.44383553"
+        "timestamp": "2025-05-22T11:51:06.198928424"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index f0109a71..d0c0e2fe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -235,7 +235,6 @@ dag {
 
 manifest {
     name            = 'nf-core/spatialxe'
-    author          = """Florian Heyl""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
         // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
         [
@@ -251,14 +250,14 @@ manifest {
     description     = """A pipeline for spatialomics Xenium data."""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=24.04.2'
+    nextflowVersion = '!>=24.10.5'
     version         = '1.0dev'
     doi             = ''
 }
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {
diff --git a/nf-test.config b/nf-test.config
index 889df760..3a1fff59 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,7 +9,7 @@ config {
     configFile "tests/nextflow.config"
 
     // ignore tests coming from the nf-core/modules repo
-    ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*'
+    ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*'
 
     // run all test with defined profile(s) from the main nextflow.config
     profile "test"
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index d23c6938..1a88aa72 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-06-03T11:01:58+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** 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/guidelines/graphic_design/workflow_diagrams#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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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": "2025-07-08T11:39:06+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** 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/guidelines/graphic_design/workflow_diagrams#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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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": "#05227869-464b-481c-b6f5-9d03620ece88"
+                    "@id": "#148b2d31-50e1-4480-8bf6-a85ca6e1a42d"
                 }
             ],
             "name": "nf-core/spatialxe"
@@ -123,7 +123,7 @@
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "dateCreated": "",
-            "dateModified": "2025-06-03T11:01:58Z",
+            "dateModified": "2025-07-08T11:39:06Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow"],
             "license": ["MIT"],
@@ -147,14 +147,14 @@
             "url": {
                 "@id": "https://www.nextflow.io/"
             },
-            "version": "!>=24.04.2"
+            "version": "!>=24.10.5"
         },
         {
-            "@id": "#05227869-464b-481c-b6f5-9d03620ece88",
+            "@id": "#148b2d31-50e1-4480-8bf6-a85ca6e1a42d",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#33cd4a92-cf89-45d4-a66c-79db7722e6f3"
+                    "@id": "#1df48a44-879c-488b-95f6-520d0a2fe3f4"
                 }
             ],
             "mainEntity": {
@@ -163,7 +163,7 @@
             "name": "Test suite for nf-core/spatialxe"
         },
         {
-            "@id": "#33cd4a92-cf89-45d4-a66c-79db7722e6f3",
+            "@id": "#1df48a44-879c-488b-95f6-520d0a2fe3f4",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/spatialxe",
             "resource": "repos/nf-core/spatialxe/actions/workflows/nf-test.yml",
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config
index 0907ac58..09ef842a 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@2.1.0"
+    id "nf-schema@2.4.2"
 }
 
 validation {
diff --git a/tests/.nftignore b/tests/.nftignore
index c10bc1f1..158c83c5 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,5 +1,6 @@
 .DS_Store
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/multiqc_data/BETA-multiqc.parquet
 multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
diff --git a/tests/nextflow.config b/tests/nextflow.config
index 580e3643..21d5c006 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -6,7 +6,9 @@
 
 // TODO nf-core: Specify any additional parameters here
 // Or any resources requirements
-params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/spatialxe'
+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/spatialxe'
+}
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

From aa9c63098a1feeba66a22b45c3e1f0bf35b6c6d1 Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Tue, 9 Sep 2025 21:16:25 +0000
Subject: [PATCH 3/8] Template update for nf-core/tools version 3.3.2

---
 ro-crate-metadata.json | 49 +++++++++++++++++++++++++++++++-----------
 1 file changed, 36 insertions(+), 13 deletions(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 1a88aa72..56724542 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-07-08T11:39:06+00:00",
+            "datePublished": "2025-09-09T21:16:18+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** 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/guidelines/graphic_design/workflow_diagrams#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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#148b2d31-50e1-4480-8bf6-a85ca6e1a42d"
+                    "@id": "#ac47eb9b-9518-4853-8e7f-d5b216ba61cb"
                 }
             ],
             "name": "nf-core/spatialxe"
@@ -121,21 +121,44 @@
         },
         {
             "@id": "main.nf",
-            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
             "dateCreated": "",
-            "dateModified": "2025-07-08T11:39:06Z",
+            "dateModified": "2025-09-09T21:16:18Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
-            "keywords": ["nf-core", "nextflow"],
-            "license": ["MIT"],
-            "name": ["nf-core/spatialxe"],
+            "keywords": [
+                "nf-core",
+                "nextflow",
+                "10x-genomics",
+                "image-processing",
+                "spatial",
+                "spatial-data-analysis",
+                "spatial-transcriptomics",
+                "transcriptomics",
+                "xenium"
+            ],
+            "license": [
+                "MIT"
+            ],
+            "name": [
+                "nf-core/spatialxe"
+            ],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": ["https://github.com/nf-core/spatialxe", "https://nf-co.re/spatialxe/dev/"],
-            "version": ["1.0dev"]
+            "url": [
+                "https://github.com/nf-core/spatialxe",
+                "https://nf-co.re/spatialxe/dev/"
+            ],
+            "version": [
+                "1.0dev"
+            ]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -150,11 +173,11 @@
             "version": "!>=24.10.5"
         },
         {
-            "@id": "#148b2d31-50e1-4480-8bf6-a85ca6e1a42d",
+            "@id": "#ac47eb9b-9518-4853-8e7f-d5b216ba61cb",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#1df48a44-879c-488b-95f6-520d0a2fe3f4"
+                    "@id": "#437782e2-7265-46ca-a751-13f80ca85b7a"
                 }
             ],
             "mainEntity": {
@@ -163,7 +186,7 @@
             "name": "Test suite for nf-core/spatialxe"
         },
         {
-            "@id": "#1df48a44-879c-488b-95f6-520d0a2fe3f4",
+            "@id": "#437782e2-7265-46ca-a751-13f80ca85b7a",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/spatialxe",
             "resource": "repos/nf-core/spatialxe/actions/workflows/nf-test.yml",
@@ -292,4 +315,4 @@
             "url": "https://nf-co.re/"
         }
     ]
-}
+}
\ No newline at end of file

From 7c3c50360b94f939205f09e56370565f8cace8fd Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Tue, 9 Sep 2025 21:20:17 +0000
Subject: [PATCH 4/8] resolving conflicts

---
 .nf-core.yml | 2 +-
 modules.json | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 6bd0fb6c..1ebce273 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,7 +8,7 @@ lint:
     - assets/nf-core-spatialxe_logo_light.png
     - docs/images/nf-core-spatialxe_logo_dark.png
     - docs/images/nf-core-spatialxe_logo_light.png
-nf_core_version: 3.2.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Florian Heyl
diff --git a/modules.json b/modules.json
index d89c6fa9..0ed5653d 100644
--- a/modules.json
+++ b/modules.json
@@ -11,6 +11,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/cellpose/cellpose.diff"
                     },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",

From 87517b74c1daeadbb8bbff46a337beaf2734e95f Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Tue, 9 Sep 2025 21:24:01 +0000
Subject: [PATCH 5/8] resolving conflicts

---
 ro-crate-metadata.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 56724542..b7dc223a 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -23,7 +23,7 @@
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
             "datePublished": "2025-09-09T21:16:18+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** 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/guidelines/graphic_design/workflow_diagrams#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/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by Florian Heyl.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-spatialxe_logo_dark.png\">\n    <img alt=\"nf-core/spatialxe\" src=\"docs/images/nf-core-spatialxe_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialxe/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/spatialxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialxe/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/spatialxe/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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/spatialxe)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![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/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. **The pipeline is currently under developement and not completed yet!**. The current plan for the pipeline implementation is shown in the metromap below. Please note that the pipeline steps and methods might change as we move forward in the development cycle.\n\n![nf-core/spatialxe-metromap](docs/images/spatialxe-metromap.png)\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n\n## Usage\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/spatialxe/results).\n\n## Pipeline summary\n\n## Quick Start\n\n`samplesheet.csv`:\n\n```csv\nsample,bundle,image\ntest_sample,/path/to/xenium-bundle,/path/to/morphology.ome.tif\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## Run image-based segmentation mode <br>\n\n`CELLPOSE -> BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode image\n```\n\n## Run coordinate-based segmentation mode <br>\n\n`PROSEG -> PROSEG2BAYSOR -> XR-IMPORT_SEGMENTATION -> SPATIALDATA -> QC`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode coordinate\n```\n\n## Run segfree mode <br>\n\n`BAYSOR_SEGFREE`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode segfree\n```\n\n## Run preview mode <br>\n\n`BAYSOR_PREVIEW`\n\n```bash\nnextflow run nf-core/spatialxe \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR> \\\n   --mode preview\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/spatialxe/usage) and the [parameter documentation](https://nf-co.re/spatialxe/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/spatialxe/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/spatialxe/output).\n\n## Credits\n\nnf-core/spatialxe was originally written by [Sameesh Kher](https://github.com/khersameesh24) and [Florian Heyl](https://github.com/heylf).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Tobias Krause\n- Kre\u0161imir Be\u0161tak (kbestak)\n- Matthias H\u00f6rtenhuber (mashehu)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (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/spatialxe 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"

From f42c9dba55b1b6f23e7bc040e738eed0db401682 Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Tue, 9 Sep 2025 21:29:05 +0000
Subject: [PATCH 6/8] fixed precommit run

---
 modules/local/proseg/proseg2baysor/main.nf                       | 1 -
 modules/local/resolift/tests/nextflow.config                     | 1 -
 subworkflows/local/cellpose_baysor_import_segmentation/main.nf   | 1 -
 subworkflows/local/ficture_preprocess_model/main.nf              | 1 -
 subworkflows/local/proseg_preset_proseg2baysor/main.nf           | 1 -
 .../xeniumranger_import_segmentation_redefine_bundle/main.nf     | 1 -
 .../local/xeniumranger_resegment_morphology_ome_tif/main.nf      | 1 -
 7 files changed, 7 deletions(-)

diff --git a/modules/local/proseg/proseg2baysor/main.nf b/modules/local/proseg/proseg2baysor/main.nf
index a3f19fc0..e841f966 100644
--- a/modules/local/proseg/proseg2baysor/main.nf
+++ b/modules/local/proseg/proseg2baysor/main.nf
@@ -51,4 +51,3 @@ process PROSEG2BAYSOR {
     END_VERSIONS
     """
 }
-
diff --git a/modules/local/resolift/tests/nextflow.config b/modules/local/resolift/tests/nextflow.config
index 5c374bf1..1a25da1b 100644
--- a/modules/local/resolift/tests/nextflow.config
+++ b/modules/local/resolift/tests/nextflow.config
@@ -6,4 +6,3 @@ process {
         ]
     }
 }
-
diff --git a/subworkflows/local/cellpose_baysor_import_segmentation/main.nf b/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
index daf6f0c9..03c358f7 100644
--- a/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
+++ b/subworkflows/local/cellpose_baysor_import_segmentation/main.nf
@@ -165,4 +165,3 @@ workflow CELLPOSE_BAYSOR_IMPORT_SEGMENTATION {
 
     versions         = ch_versions                                 // channel: [ versions.yml ]
 }
-
diff --git a/subworkflows/local/ficture_preprocess_model/main.nf b/subworkflows/local/ficture_preprocess_model/main.nf
index bf8e259a..a43e61ca 100644
--- a/subworkflows/local/ficture_preprocess_model/main.nf
+++ b/subworkflows/local/ficture_preprocess_model/main.nf
@@ -50,4 +50,3 @@ workflow FICTURE_PREPROCESS_MODEL {
 
     versions = ch_versions                                          // channel: [ versions.yml ]
 }
-
diff --git a/subworkflows/local/proseg_preset_proseg2baysor/main.nf b/subworkflows/local/proseg_preset_proseg2baysor/main.nf
index 57b761a8..5694de59 100644
--- a/subworkflows/local/proseg_preset_proseg2baysor/main.nf
+++ b/subworkflows/local/proseg_preset_proseg2baysor/main.nf
@@ -60,4 +60,3 @@ workflow PROSEG_PRESET_PROSEG2BAYSOR {
 
     versions              = ch_versions                                 // channel: [ versions.yml ]
 }
-
diff --git a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
index 766e119e..2731f4df 100644
--- a/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
+++ b/subworkflows/local/xeniumranger_import_segmentation_redefine_bundle/main.nf
@@ -103,4 +103,3 @@ workflow XENIUMRANGER_IMPORT_SEGMENTATION_REDEFINE_BUNDLE {
 
     versions          = ch_versions         // channel: [ versions.yml ]
 }
-
diff --git a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
index c41e8bdb..84b00a06 100644
--- a/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
+++ b/subworkflows/local/xeniumranger_resegment_morphology_ome_tif/main.nf
@@ -56,4 +56,3 @@ workflow XENIUMRANGER_RESEGMENT_MORPHOLOGY_OME_TIF {
 
     versions = ch_versions                 // channel: [ versions.yml ]
 }
-

From 1ce65b2131641d2173e7247a4baa7c37931690aa Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Tue, 9 Sep 2025 21:32:15 +0000
Subject: [PATCH 7/8] fix nf-core linting errors

---
 modules.json                                  |  2 +-
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 ++--
 .../nf-core/multiqc/tests/main.nf.test.snap   | 24 +++++++++----------
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/modules.json b/modules.json
index 0ed5653d..a0eb1a42 100644
--- a/modules.json
+++ b/modules.json
@@ -18,7 +18,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
+                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     },
                     "untar": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d430da5f..dd513cbd 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=1.28
+  - bioconda::multiqc=1.31
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index f3b57047..5288f5cc 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.28--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.28--pyhdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
+        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 26d74307..17881d15 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T16:05:18.927925"
+        "timestamp": "2025-09-08T20:57:36.139055243"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T16:05:55.639955"
+        "timestamp": "2025-09-08T20:59:15.142230631"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,b05075d2d2b4f485c0d627a5c8e475b2"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-03-26T16:05:44.067369"
+        "timestamp": "2025-09-08T20:58:29.629087066"
     }
 }
\ No newline at end of file

From 8ef79b8d003ef4ebc71defabc8083ce3462bcd90 Mon Sep 17 00:00:00 2001
From: Sameesh Kher <khersameesh24@gmail.com>
Date: Wed, 10 Sep 2025 10:34:13 +0000
Subject: [PATCH 8/8] removed fastqc

---
 modules.json                                  |  5 --
 .../proseg/proseg2baysor/tests/main.nf.test   |  2 +-
 modules/nf-core/fastqc/environment.yml        |  7 --
 modules/nf-core/fastqc/main.nf                | 64 -----------------
 modules/nf-core/fastqc/meta.yml               | 72 -------------------
 tests/.nftignore                              |  1 -
 6 files changed, 1 insertion(+), 150 deletions(-)
 delete mode 100644 modules/nf-core/fastqc/environment.yml
 delete mode 100644 modules/nf-core/fastqc/main.nf
 delete mode 100644 modules/nf-core/fastqc/meta.yml

diff --git a/modules.json b/modules.json
index a0eb1a42..2617b954 100644
--- a/modules.json
+++ b/modules.json
@@ -11,11 +11,6 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/cellpose/cellpose.diff"
                     },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
diff --git a/modules/local/proseg/proseg2baysor/tests/main.nf.test b/modules/local/proseg/proseg2baysor/tests/main.nf.test
index 88fdc127..aa4d645c 100644
--- a/modules/local/proseg/proseg2baysor/tests/main.nf.test
+++ b/modules/local/proseg/proseg2baysor/tests/main.nf.test
@@ -21,7 +21,7 @@ nextflow_process {
                 }
             }
             run("PROSEG") {
-                script "modules/local/proseg/proseg/main.nf"
+                script "modules/local/proseg/preset/main.nf"
                 process {
                     """
                     input[0] = Channel.of([
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
deleted file mode 100644
index f9f54ee9..00000000
--- a/modules/nf-core/fastqc/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
deleted file mode 100644
index 23e16634..00000000
--- a/modules/nf-core/fastqc/main.nf
+++ /dev/null
@@ -1,64 +0,0 @@
-process FASTQC {
-    tag "${meta.id}"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
-        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args          = task.ext.args ?: ''
-    def prefix        = task.ext.prefix ?: "${meta.id}"
-    // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to     = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ')
-
-    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
-    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
-    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
-    def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null
-    // FastQC memory value allowed range (100 - 10000)
-    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
-
-    """
-    printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
-        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
-    done
-
-    fastqc \\
-        ${args} \\
-        --threads ${task.cpus} \\
-        --memory ${fastqc_memory} \\
-        ${renamed_files}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.html
-    touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
deleted file mode 100644
index c8d9d025..00000000
--- a/modules/nf-core/fastqc/meta.yml
+++ /dev/null
@@ -1,72 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-  - quality control
-  - qc
-  - adapters
-  - fastq
-tools:
-  - fastqc:
-      description: |
-        FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
-
-        You get information about adapter contamination and other
-        overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-      licence: ["GPL-2.0-only"]
-      identifier: biotools:fastqc
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-          respectively.
-        ontologies: []
-output:
-  html:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.html":
-          type: file
-          description: FastQC report
-          pattern: "*_{fastqc.html}"
-          ontologies: []
-  zip:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.zip":
-          type: file
-          description: FastQC report archive
-          pattern: "*_{fastqc.zip}"
-          ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
-authors:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
-maintainers:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
diff --git a/tests/.nftignore b/tests/.nftignore
index 158c83c5..197c20ca 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -7,5 +7,4 @@ multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
-fastqc/*_fastqc.{html,zip}
 pipeline_info/*.{html,json,txt,yml}