nf-core · heylf · Nov 20, 2025 · Apr 30, 2026 · May 8, 2026 · May 8, 2026
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -8,14 +8,14 @@ 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/spatialaxe/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/spatialaxe/tree/master/docs/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/spatialaxe/tree/main/.github/CONTRIBUTING.md)
+- [ ] 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/docs/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>`).

diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -32,9 +32,28 @@ jobs:
           compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
           workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/spatialaxe/work-${{ steps.revision.outputs.revision }}
+          nextflow_config: |
+            plugins {
+              id 'nf-slack@0.5.0'
+            }
+            slack {
+              enabled = true
+              bot {
+                token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
+                channel = 'spatialaxe'
+              }
+              onStart {
+                enabled = false
+              }
+              onComplete {
+                message = ':white_check_mark: *spatialaxe/test_full* completed successfully! :tada:'
+              }
+              onError {
+                message = ':x: *spatialaxe/test_full* failed :crying_cat_face:'
+              }
+            }
           parameters: |
             {
-              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/spatialaxe/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -11,54 +11,50 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
-        with:
-          python-version: "3.14"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
           python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@master
+      - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -10,9 +10,7 @@ lint:
     - docs/images/nf-core-spatialaxe_logo_dark.png
     - docs/images/nf-core-spatialaxe_logo_light.png
     - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/workflows/branch.yml
-    - .github/workflows/linting.yml
-nf_core_version: 3.5.2
+nf_core_version: 4.0.3
 repository_type: pipeline
 template:
   author: Sameesh Kher, Dongze He, Florian Heyl
@@ -24,4 +22,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 1.0.0
+  version: 1.0.1
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,24 @@
 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).
 
-## v1.0.0 - [date]
+## 1.0.1 - [31.07.2026]
+
+Hotfix to tackle some bugs
+
+### `Added`
+
+- Template update for nf-core/tools version 4.0.3
+
+### `Fixed`
+
+- Only pass `--expansion-distance` to `xeniumranger import-segmentation` for nuclei-based imports. It was applied to every import, but xeniumranger rejects it for transcript-assignment imports (proseg/baysor/segger) and cells-only imports with `ERROR: --expansion-distance requires --nuclei`.
+- Preserve the URI scheme (e.g. `s3://`) when building Xenium bundle child paths, so bundle validation works when the work directory is on object storage (S3/GCS/Azure). Previously `Path.toString()` dropped the scheme and the resulting path was resolved on the local filesystem, causing `Xenium bundle does not exist` / `NoSuchFileException` failures on AWS Batch.
+
+### `Dependencies`
+
+### `Deprecated`
+
+## 1.0.0 - [18.06.2026]
 
 Initial release of nf-core/spatialaxe, created with the [nf-core](https://nf-co.re/) template.
 

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/spatialaxe)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/spatialaxe)
 [![GitHub Actions CI Status](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/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/spatialaxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.20733817-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.20733817)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/spatialaxe/releases/tag/1.0.0" target="_blank">nf-core/spatialaxe</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/spatialaxe/1.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/spatialaxe/releases/tag/1.0.1" target="_blank">nf-core/spatialaxe</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/spatialaxe/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-spatialaxe-methods-description":
     order: -1000

diff --git a/assets/nf-core-spatialaxe_logo_light.png b/assets/nf-core-spatialaxe_logo_light.png
diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock' } }
diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock' } }
diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' } }
diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8' } }
diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' } }
diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data' } }
diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d' } }
diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config
@@ -0,0 +1 @@
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2' } }
diff --git a/conf/modules.config b/conf/modules.config
@@ -82,9 +82,6 @@ process {
             path: "${params.outdir}/${params.mode}/xeniumranger/import_segementation",
             mode: params.publish_dir_mode,
         ]
-        ext.args = {[
-            params.expansion_distance != null ? "--expansion-distance=${params.expansion_distance}" : "",
-        ].join(' ').trim()}
     }
 
     // ---------------------------- proseg ---------------------------------------------------
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		process { withName: 'MULTIQC' { container = 'https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock' } }