nf-core · nf-core-bot · Jul 24, 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/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/docs/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/spatialxe/tree/master/docs/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/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>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,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@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
+      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

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
@@ -32,7 +32,7 @@ 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-${{ steps.revision.outputs.revision }}
           nextflow_config: |
             plugins {
               id 'nf-slack@0.5.0'
@@ -41,21 +41,21 @@ jobs:
               enabled = true
               bot {
                 token = '${{ secrets.NFSLACK_BOT_TOKEN }}'
-                channel = 'spatialxe'
+                channel = 'spatialaxe'
               }
               onStart {
                 enabled = false
               }
               onComplete {
-                message = ':white_check_mark: *spatialxe/test_full* completed successfully! :tada:'
+                message = ':white_check_mark: *spatialaxe/test_full* completed successfully! :tada:'
               }
               onError {
-                message = ':x: *spatialxe/test_full* failed :crying_cat_face:'
+                message = ':x: *spatialaxe/test_full* failed :crying_cat_face:'
               }
             }
           parameters: |
             {
-              "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
 

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
@@ -18,10 +18,10 @@ 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
 

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -2,45 +2,61 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to `main`/`master` branch on the repository
 # It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
-  pull_request_target:
+  pull_request:
     branches:
       - main
       - master
 
+permissions: {}
+
 jobs:
   test:
     runs-on: ubuntu-latest
     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'
+        env:
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialxe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ "$HEAD_REPO" == 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
-      - name: Post PR comment
+      # If the above check failed, build a comment to be posted by the shared poster workflow
+      - name: Build PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
-        with:
-          message: |
-            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          BASE_REF: ${{ github.event.pull_request.base.ref }}
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
+          PR_USER: ${{ github.event.pull_request.user.login }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "branch" > pr-comment/header.txt
+          cat > pr-comment/comment.md <<EOF
+          ## This PR is against the \`${BASE_REF}\` branch :x:
 
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
+          * Do not close this PR
+          * Click _Edit_ and change the \`base\` to \`dev\`
+          * This CI test will remain failed until you push a new commit
 
-            ---
+          ---
 
-            Hi @${{ github.event.pull_request.user.login }},
+          Hi @${PR_USER},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
-            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+          It looks like this pull-request is has been made against the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) ${BASE_REF} branch.
+          The ${BASE_REF} branch on nf-core repositories should always contain code from the latest release.
+          Because of this, PRs to ${BASE_REF} are only allowed if they come from the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) \`dev\` branch.
 
-            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
-            Note that even after this, the test will continue to show as failing until you push a new commit.
+          You do not need to close this PR, you can change the target branch to \`dev\` by clicking the _"Edit"_ button at the top of this page.
+          Note that even after this, the test will continue to show as failing until you push a new commit.
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+          Thanks again for your contribution!
+          EOF
+
+      - name: Upload PR comment artifact
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
@@ -9,7 +9,7 @@ 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
@@ -82,4 +82,4 @@ 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
@@ -74,3 +74,21 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "lint" > pr-comment/header.txt
+          [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -116,6 +116,22 @@ jobs:
             fi
           fi
 
+      # continue-on-error keeps latest-everything from failing the job, so it never shows up in
+      # `needs.nf-test.result` downstream and CI stays green. Surface it via a PR comment instead;
+      # other NXF_VER failures already fail the job/CI directly, so no comment is needed for those.
+      - name: Prepare PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        run: |
+          mkdir -p pr-comment-fragment
+          echo "* ❌ \`${{ matrix.profile }}\` | \`${{ matrix.NXF_VER }}\` | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" > pr-comment-fragment/fragment.md
+
+      - name: Upload PR comment fragment
+        if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment-fragment-${{ strategy.job-index }}
+          path: pr-comment-fragment/
+
   confirm-pass:
     needs: [nf-test]
     if: always()
@@ -142,3 +158,44 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
+
+      - name: Download PR comment fragments
+        if: ${{ always() }}
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        continue-on-error: true
+        with:
+          pattern: pr-comment-fragment-*
+          path: pr-comment-fragments
+          merge-multiple: true
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR.
+      # Based on the fragments above (not needs.*.result) so non-blocking failures are still reported.
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "nf-test" > pr-comment/header.txt
+          if [ -d pr-comment-fragments ] && [ -n "$(ls -A pr-comment-fragments)" ]; then
+            {
+              echo "## ❌ nf-test failed with latest Nextflow version"
+              echo ""
+              echo "> [!NOTE]"
+              echo "> Tests with Nextflow's latest version failed but it will not cause a CI workflow failure."
+              echo "> Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing."
+              echo ""
+              cat pr-comment-fragments/*.md
+              echo ""
+              echo "See the [full run](${RUN_URL}) for details."
+            } > pr-comment/comment.md
+          fi
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/