heylf · heylf · Nov 20, 2025 · Apr 30, 2026 · May 27, 2026 · May 27, 2026
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
@@ -10,4 +10,4 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 nextflow self-update
 
 # Update welcome message
-echo "Welcome to the nf-core/spatialxe devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
+echo "Welcome to the nf-core/spatialaxe devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,23 +1,23 @@
-# `nf-core/spatialxe`: Contributing Guidelines
+# `nf-core/spatialaxe`: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/spatialxe.
+Many thanks for taking an interest in improving nf-core/spatialaxe.
 
-We try to manage the required tasks for nf-core/spatialxe using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-core/spatialaxe using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 > [!NOTE]
-> If you need help using or modifying nf-core/spatialxe then the best place to ask is on the nf-core Slack [#spatialxe](https://nfcore.slack.com/channels/spatialxe) channel ([join our Slack here](https://nf-co.re/join/slack)).
+> If you need help using or modifying nf-core/spatialaxe then the best place to ask is on the nf-core Slack [#spatialaxe](https://nfcore.slack.com/channels/spatialaxe) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/spatialxe, the standard workflow is as follows:
+If you'd like to write some code for nf-core/spatialaxe, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/spatialxe issues](https://github.com/nf-core/spatialxe/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/spatialxe repository](https://github.com/nf-core/spatialxe) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-core/spatialaxe issues](https://github.com/nf-core/spatialaxe/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/spatialaxe repository](https://github.com/nf-core/spatialaxe) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -61,11 +61,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/spatialxe documentation](https://nf-co.re/spatialxe/usage) and don't hesitate to get in touch on the nf-core Slack [#spatialxe](https://nfcore.slack.com/channels/spatialxe) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/spatialaxe documentation](https://nf-co.re/spatialaxe/usage) and don't hesitate to get in touch on the nf-core Slack [#spatialaxe](https://nfcore.slack.com/channels/spatialaxe) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the `nf-core/spatialxe` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/spatialaxe` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -115,7 +115,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/spatialxe/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-core/spatialaxe/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/spatialxe pipeline documentation](https://nf-co.re/spatialxe/usage)
+        - [nf-core/spatialaxe pipeline documentation](https://nf-co.re/spatialaxe/usage)
   - type: textarea
     id: description
     attributes:
@@ -46,4 +46,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/spatialxe _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-core/spatialaxe _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -2,6 +2,6 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: "Slack #spatialxe channel"
-    url: https://nfcore.slack.com/channels/spatialxe
-    about: Discussion about the nf-core/spatialxe pipeline
+  - name: "Slack #spatialaxe channel"
+    url: https://nfcore.slack.com/channels/spatialaxe
+    about: Discussion about the nf-core/spatialaxe pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/spatialxe pipeline
+description: Suggest an idea for the nf-core/spatialaxe pipeline
 labels: enhancement
 body:
   - type: textarea

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,22 +1,22 @@
 <!--
-# nf-core/spatialxe pull request
+# nf-core/spatialaxe pull request
 
-Many thanks for contributing to nf-core/spatialxe!
+Many thanks for contributing to nf-core/spatialaxe!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/spatialxe/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/spatialaxe/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/spatialxe/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/spatialxe _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/spatialaxe/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/spatialaxe _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

diff --git 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' || github.event_name == 'release'
+    if: github.repository == 'nf-core/spatialaxe' && 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
@@ -32,15 +32,15 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/spatialxe/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/spatialaxe/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/spatialxe/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/spatialaxe/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -7,7 +7,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS tests
-    if: github.repository == 'nf-core/spatialxe'
+    if: github.repository == 'nf-core/spatialaxe'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Seqera Platform CLI tool action
@@ -18,14 +18,14 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/spatialxe/work-${{ github.sha }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/spatialaxe/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/spatialxe/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/spatialaxe/results-test-${{ github.sha }}"
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,9 +13,9 @@ jobs:
     steps:
       # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/spatialxe'
+        if: github.repository == 'nf-core/spatialaxe'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialxe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialaxe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
@@ -9,11 +9,11 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/spatialxe'
+      github.repository == 'nf-core/spatialaxe'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/nf-core/spatialxe/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/nf-core/spatialaxe/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -85,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -15,10 +15,9 @@ jobs:
           echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics

diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -7,14 +7,17 @@ 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: 3.4.1
+    - .github/PULL_REQUEST_TEMPLATE.md
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
-  author: Sameesh Kher, Florian Heyl
+  author: Sameesh Kher, Dongze He, Florian Heyl
   description: A pipeline for spatialomics Xenium In Situ data.
   force: false
   is_nfcore: true
-  name: spatialxe
+  name: spatialaxe
   org: nf-core
   outdir: .
-  version: 1.0dev
+  skip_features:
+    - igenomes
+  version: 1.0.0
diff --git a/.prettierignore b/.prettierignore
@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,11 +1,11 @@
-# nf-core/spatialxe: Changelog
+# nf-core/spatialaxe: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v1.0.0 - [date]
 
-Initial release of nf-core/spatialxe, created with the [nf-core](https://nf-co.re/) template.
+Initial release of nf-core/spatialaxe, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,4 +1,4 @@
-# nf-core/spatialxe: Citations
+# nf-core/spatialaxe: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) The nf-core/spatialxe team
+Copyright (c) The nf-core/spatialaxe team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal