nf-core · mashehu · Oct 5, 2023 · Oct 5, 2023 · Oct 5, 2023 · Oct 5, 2023
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -49,6 +49,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v3
+        with:
+          node-version: 20
 
       - name: Install Prettier
         run: npm install -g prettier

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -19,7 +19,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -52,6 +52,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v3
+        with:
+          node-version: 20
 
       - name: Install Prettier
         run: npm install -g prettier

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -6,6 +6,7 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 # Cancel if a newer run is started
 concurrency:
@@ -17,7 +18,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -31,6 +32,8 @@ jobs:
 
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
+        env:
+          AGENT_TOOLSDIRECTORY: ${{ runner.tool_cache }}
         with:
           python-version: 3.11
 
@@ -46,12 +49,14 @@ jobs:
 
       - name: Run nf-core/tools
         run: |
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
-          nextflow run nf-core-testpipeline -profile test,docker --outdir ./results
+          echo "docker.userEmulation = false" > aws_docker.config
+          echo "docker.fixOwnership = true" >> aws_docker.config
+          nf-core --verbose --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+          nextflow run nf-core-testpipeline -profile test,docker -c aws_docker.config --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}
         uses: actions/upload-artifact@v3
         with:
           name: nf-core-log-file
-          path: log.txt
+          path: .nextflow.log
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -10,7 +10,7 @@ jobs:
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
       github.repository == 'nf-core/tools'
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@v3
@@ -25,6 +25,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - uses: actions/setup-node@v3
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -42,6 +44,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
+
       - name: python-isort
         uses: isort/[email protected]
         with:

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
@@ -14,11 +14,13 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - uses: actions/checkout@v3
 
       - uses: actions/setup-node@v3
+        with:
+          node-version: 20
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -28,11 +30,13 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - uses: actions/checkout@v3
 
       - uses: actions/setup-node@v3
+        with:
+          node-version: 20
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -41,7 +45,7 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - uses: actions/checkout@v3
 
@@ -71,7 +75,7 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v3

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         python-version: ["3.8", "3.11"]
-        runner: ["ubuntu-latest"]
+        runner: ["self-hosted"]
         include:
           - runner: "ubuntu-20.04"
             python-version: "3.8"

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -16,7 +16,7 @@ concurrency:
 
 jobs:
   get-pipelines:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     outputs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
@@ -31,7 +31,7 @@ jobs:
 
   sync:
     needs: get-pipelines
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     strategy:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false