From fed2e9b56b40c2fabaf0f166a3d05948c85209c3 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Tue, 14 Dec 2021 15:58:59 +0100 Subject: [PATCH 1/3] fix gh wf workflow --- .github/workflows/create-lint-wf.yml | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index d7cff18e29..d714477651 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -1,6 +1,10 @@ name: Create a pipeline and lint it on: [push, pull_request] +env: + NXF_ANSI_LOG: false + CAPSULE_LOG: none + jobs: MakeTestWorkflow: runs-on: ubuntu-latest @@ -8,8 +12,14 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - # Nextflow versions: check pipeline minimum and latest edge version - nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"] + # Nextflow versions + include: + # Test pipeline minimum Nextflow version + - NXF_VER: '21.10.3' + NXF_EDGE: '' + # Test latest edge release of Nextflow + - NXF_VER: '' + NXF_EDGE: '1' steps: - uses: actions/checkout@v2 name: Check out source-code repository @@ -26,12 +36,13 @@ jobs: - name: Install Nextflow env: - CAPSULE_LOG: none + NXF_VER: ${{ matrix.NXF_VER }} + # Uncomment only if the edge release is more recent than the latest stable release + # See https://github.com/nextflow-io/nextflow/issues/2467 + # NXF_EDGE: ${{ matrix.NXF_EDGE }} run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - export ${{ matrix.nxf_ver }} - nextflow self-update - name: nf-core create run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" From f51c46299e912ed17d6937c75d349374485508ed Mon Sep 17 00:00:00 2001 From: ggabernet Date: Tue, 14 Dec 2021 16:00:30 +0100 Subject: [PATCH 2/3] fix test wf --- .github/workflows/create-test-wf.yml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 4aa24e0894..9b13cadd39 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -1,6 +1,10 @@ name: Create a pipeline and test it on: [push, pull_request] +env: + NXF_ANSI_LOG: false + CAPSULE_LOG: none + jobs: RunTestWorkflow: runs-on: ubuntu-latest @@ -8,10 +12,14 @@ jobs: NXF_ANSI_LOG: false strategy: matrix: - # Nextflow versions: check pipeline minimum and latest edge version - nxf_ver: - - "NXF_VER=21.10.3" - # - "NXF_EDGE=1" + # Nextflow versions + include: + # Test pipeline minimum Nextflow version + - NXF_VER: '21.10.3' + NXF_EDGE: '' + # Test latest edge release of Nextflow + - NXF_VER: '' + NXF_EDGE: '1' steps: - uses: actions/checkout@v2 name: Check out source-code repository @@ -28,12 +36,13 @@ jobs: - name: Install Nextflow env: - CAPSULE_LOG: none + NXF_VER: ${{ matrix.NXF_VER }} + # Uncomment only if the edge release is more recent than the latest stable release + # See https://github.com/nextflow-io/nextflow/issues/2467 + # NXF_EDGE: ${{ matrix.NXF_EDGE }} run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - export ${{ matrix.nxf_ver }} - nextflow self-update - name: Run nf-core/tools run: | From cc54b9e7cccaec61acb99f35bf97e1722cc00f83 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Tue, 14 Dec 2021 16:03:25 +0100 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a4dde35113..93ec4fa4a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,7 @@ * Erase temporary files and folders while performing Python tests (pytest) * Remove base `Dockerfile` used for DSL1 pipeline container builds * Run tests with Python 3.10 +* [#1363](https://github.com/nf-core/tools/pull/1363) Fix tools CI workflow nextflow versions. ### Modules