Merge pull request #3546 from mirpedrol/patch-3.2.1

merge to main for patch 3.2.1

Author: mirpedrol

CHANGELOG.md

@@ -1,5 +1,13 @@
 # nf-core/tools: Changelog
 
+## [v3.2.1 - Pewter Pangolin Patch](https://github.com/nf-core/tools/releases/tag/3.2.1) - [2025-04-29]
+
+### Template
+
+- Run awsfulltest after release, and with dev revision on PRs to master/main ([#3485](https://github.com/nf-core/tools/pull/3485))
+- Downgrade nf-schema to fix CI tests ([#3544](https://github.com/nf-core/tools/pull/3544))
+- Fail nextflow run test gracefully for `latest everything` ([#3543](https://github.com/nf-core/tools/pull/3543))
+
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 
 ### Template

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -4,60 +4,39 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/[email protected]
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/{%- raw -%}${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'{% endraw %}
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision={%- raw -%}${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters {%- raw %}
+        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ steps.revision.outputs.revision }}{% endraw %}
           parameters: |
             {
               "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
-              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
+              "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ steps.revision.outputs.revision }}{% endraw %}"
             }
           profiles: test_full
 

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -83,5 +83,6 @@ jobs:
         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{% endraw %}

nf_core/pipeline-template/nextflow.config

@@ -295,7 +295,7 @@ manifest {
 {% if nf_schema -%}
 // 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@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

nf_core/pipelines/lint/actions_awsfulltest.py

@@ -42,12 +42,12 @@ def actions_awsfulltest(self) -> Dict[str, List[str]]:
 
         # Check that the action is only turned on for published releases
         try:
-            if wf[True]["pull_request"]["branches"] != ["main", "master"]:
-                raise AssertionError()
             if wf[True]["pull_request_review"]["types"] != ["submitted"]:
                 raise AssertionError()
             if "workflow_dispatch" not in wf[True]:
                 raise AssertionError()
+            if wf[True]["release"]["types"] != ["published"]:
+                raise AssertionError()
         except (AssertionError, KeyError, TypeError):
             failed.append("`.github/workflows/awsfulltest.yml` is not triggered correctly")
         else:

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.2.0"
+version = "3.2.1"
 
 with open("README.md") as f:
     readme = f.read()

tests/utils.py

@@ -30,7 +30,7 @@
 GITLAB_BRANCH_ORG_PATH_BRANCH = "org-path"
 GITLAB_BRANCH_TEST_OLD_SHA = "e772abc22c1ff26afdf377845c323172fb3c19ca"
 GITLAB_BRANCH_TEST_NEW_SHA = "7d73e21f30041297ea44367f2b4fd4e045c0b991"
-GITLAB_NFTEST_BRANCH = "nf-test-tests-self-hosted-runners"
+GITLAB_NFTEST_BRANCH = "nf-test-tests-old"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]: