From ef3a1bbe5e5c5471a5ba82e74ff80340361146a7 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Wed, 4 Dec 2024 17:01:20 +0000 Subject: [PATCH 1/3] Splitting up tests --- .github/workflows/end-to-end.yml | 62 ++++++++++++++++++++++++++------ 1 file changed, 51 insertions(+), 11 deletions(-) diff --git a/.github/workflows/end-to-end.yml b/.github/workflows/end-to-end.yml index 1f9d3d9..18433a6 100644 --- a/.github/workflows/end-to-end.yml +++ b/.github/workflows/end-to-end.yml @@ -3,8 +3,9 @@ name: End-to-end MGS workflow test on: [pull_request] jobs: - test: + test-index: runs-on: ubuntu-latest + timeout-minutes: 10 steps: - name: Checkout @@ -16,10 +17,10 @@ jobs: java-version: '11' distribution: 'adopt' - - name: Setup Nextflow latest (stable) + - name: Setup Nextflow latest-edge uses: nf-core/setup-nextflow@v1 with: - version: "latest" + version: "latest-edge" - name: Install nf-test run: | @@ -28,19 +29,58 @@ jobs: - name: Run index workflow run: nf-test test --tag index --verbose + test-run: + runs-on: ubuntu-latest + timeout-minutes: 10 - - name: Clean docker for more space - run: | - docker kill $(docker ps -q) 2>/dev/null || true - docker rm $(docker ps -a -q) 2>/dev/null || true - docker rmi $(docker images -q) -f 2>/dev/null || true - docker system prune -af --volumes + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up JDK 11 + uses: actions/setup-java@v4 + with: + java-version: '11' + distribution: 'adopt' - - name: Clean up nf-test dir - run: sudo rm -rf .nf-test + - name: Setup Nextflow latest-edge + uses: nf-core/setup-nextflow@v1 + with: + version: "latest-edge" + + - name: Install nf-test + run: | + wget -qO- https://get.nf-test.com | bash + sudo mv nf-test /usr/local/bin/ - name: Run run workflow run: nf-test test --tag run --verbose - name: Run run_validation workflow run: nf-test test --tag validation --verbose + test-validation: + runs-on: ubuntu-latest + timeout-minutes: 5 + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up JDK 11 + uses: actions/setup-java@v4 + with: + java-version: '11' + distribution: 'adopt' + + - name: Setup Nextflow latest-edge + uses: nf-core/setup-nextflow@v1 + with: + version: "latest-edge" + + - name: Install nf-test + run: | + wget -qO- https://get.nf-test.com | bash + sudo mv nf-test /usr/local/bin/ + + - name: Run run_validation workflow + run: nf-test test --tag validation --verbose \ No newline at end of file From 67742e8ea85b686a639921445ef55ccb99024193 Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Wed, 4 Dec 2024 17:03:32 +0000 Subject: [PATCH 2/3] Didn't know that I had an out of date verison of this branch. --- .github/workflows/end-to-end.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/end-to-end.yml b/.github/workflows/end-to-end.yml index 18433a6..859a26a 100644 --- a/.github/workflows/end-to-end.yml +++ b/.github/workflows/end-to-end.yml @@ -17,10 +17,10 @@ jobs: java-version: '11' distribution: 'adopt' - - name: Setup Nextflow latest-edge + - name: Setup Nextflow latest (stable) uses: nf-core/setup-nextflow@v1 with: - version: "latest-edge" + version: "latest" - name: Install nf-test run: | @@ -43,10 +43,10 @@ jobs: java-version: '11' distribution: 'adopt' - - name: Setup Nextflow latest-edge + - name: Setup Nextflow latest (stable) uses: nf-core/setup-nextflow@v1 with: - version: "latest-edge" + version: "latest" - name: Install nf-test run: | @@ -72,10 +72,10 @@ jobs: java-version: '11' distribution: 'adopt' - - name: Setup Nextflow latest-edge + - name: Setup Nextflow latest (stable) uses: nf-core/setup-nextflow@v1 with: - version: "latest-edge" + version: "latest" - name: Install nf-test run: | From 8ae0a930d24d729eef9ce05a69a9663be8626a8a Mon Sep 17 00:00:00 2001 From: EC2 Default User Date: Wed, 4 Dec 2024 17:07:10 +0000 Subject: [PATCH 3/3] Forgot to remove validation from run test, hopefully this will test the timeout as well. --- .github/workflows/end-to-end.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/end-to-end.yml b/.github/workflows/end-to-end.yml index 859a26a..a044fea 100644 --- a/.github/workflows/end-to-end.yml +++ b/.github/workflows/end-to-end.yml @@ -56,8 +56,6 @@ jobs: - name: Run run workflow run: nf-test test --tag run --verbose - - name: Run run_validation workflow - run: nf-test test --tag validation --verbose test-validation: runs-on: ubuntu-latest timeout-minutes: 5