Merge branch 'dev' into fix-output-detection-in-lint-3513

Author: mashehu

.github/workflows/create-lint-wf.yml

@@ -15,14 +15,6 @@ on:
   release:
     types: [published]
   workflow_dispatch:
-    inputs:
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
 
 # Cancel if a newer run is started
 concurrency:
@@ -31,7 +23,9 @@ concurrency:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-make-test-worfklow
+      - runner=4cpu-linux-x64
     env:
       NXF_ANSI_LOG: false
 

.github/workflows/create-test-lint-wf-template.yml

@@ -14,14 +14,6 @@ on:
   release:
     types: [published]
   workflow_dispatch:
-    inputs:
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
 
 # Cancel if a newer run is started
 concurrency:
@@ -49,28 +41,18 @@ jobs:
           echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT
 
   RunTestWorkflow:
-    runs-on: ${{ matrix.runner }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-run-test-worfklow
+      - runner=4cpu-linux-x64
     needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
 
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}
-        runner:
-          # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
-          - ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
-        profile: ["self_hosted_runner"]
         include:
           - TEMPLATE: all
-            runner: ubuntu-latest
-            profile: "docker"
-          - TEMPLATE: nf_core_configs
-            runner: ubuntu-latest
-            profile: "docker"
-        exclude:
-          - TEMPLATE: nf_core_configs
-            profile: "self_hosted_runner"
       fail-fast: false
 
     steps:
@@ -119,7 +101,7 @@ jobs:
       - name: run the pipeline
         run: |
           cd create-test-lint-wf
-          nextflow run my-prefix-testpipeline -profile test,${{matrix.profile}} --outdir ./results
+          nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results
 
       # Remove results folder before linting
       - name: remove results folder

.github/workflows/create-test-wf.yml

@@ -15,14 +15,6 @@ on:
   release:
     types: [published]
   workflow_dispatch:
-    inputs:
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
 
 # Cancel if a newer run is started
 concurrency:
@@ -31,8 +23,9 @@ concurrency:
 
 jobs:
   RunTestWorkflow:
-    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
-    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-run-test-worfklow
+      - runner=4cpu-linux-x64
     env:
       NXF_ANSI_LOG: false
 
@@ -71,7 +64,7 @@ jobs:
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
           nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          nextflow run nf-core-testpipeline -profile self_hosted_runner,test --outdir ./results
+          nextflow run nf-core-testpipeline -profile docker,test --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

.github/workflows/pytest.yml

@@ -20,14 +20,6 @@ on:
   release:
     types: [published]
   workflow_dispatch:
-    inputs:
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
 
 # Cancel if a newer run with the same workflow name is queued
 concurrency:
@@ -77,8 +69,9 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    # run on self-hosted runners for test_components_generate_snapshot.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
-    runs-on: ${{ matrix.test == 'components/test_components_generate_snapshot.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-run-test
+      - runner=4cpu-linux-x64
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails
@@ -166,8 +159,9 @@ jobs:
 
   coverage:
     needs: test
-    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
-    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-coverage
+      - runner=2cpu-linux-x64
     steps:
       - name: go to subdirectory
         run: |

.github/workflows/sync.yml

@@ -8,13 +8,6 @@ on:
         type: boolean
         description: Only run on nf-core/testpipeline?
         required: true
-      runners:
-        description: "Runners to test on"
-        type: choice
-        options:
-          - "ubuntu-latest"
-          - "self-hosted"
-        default: "self-hosted"
       force_pr:
         description: "Force a PR to be created"
         type: boolean
@@ -58,8 +51,9 @@ jobs:
 
   sync:
     needs: get-pipelines
-    # use the github runner on release otherwise use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
-    runs-on: ${{github.event_name == 'release' && 'self-hosted' || github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    runs-on:
+      - runs-on=${{ github.run_id }}-sync
+      - runner=4cpu-linux-x64
     strategy:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false

CHANGELOG.md

@@ -61,6 +61,7 @@
 - Fix indentation in included_configs API docs ([#3523](https://github.com/nf-core/tools/pull/3523))
 - chore(deps): update python:3.12-slim docker digest to a866731 ([#3527](https://github.com/nf-core/tools/pull/3527))
 - adding boundary in regex ([#3535](https://github.com/nf-core/tools/pull/3535))
+- switch to using runsOn runners in nf-core/tools repo ([#3537](https://github.com/nf-core/tools/pull/3537))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 

tests/utils.py

@@ -32,7 +32,7 @@
 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"
 
 
 def with_temporary_folder(func: Callable[..., Any]) -> Callable[..., Any]: