From 504eff9e0458d3f3f432b2c3e5f571982a7a92b4 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 12:35:10 +0000 Subject: [PATCH 1/6] update actions --- .github/workflows/continuous_integration.yml | 25 ++++++++------------ 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index d01a2b98..8beea47f 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -18,7 +18,9 @@ jobs: strategy: matrix: - nxf_ver: ['21.10.6', ''] + NXF_VER: + - '22.10.1' + - 'latest' profile: - docker workflow: @@ -29,22 +31,15 @@ jobs: # Steps represent a sequence of tasks that will be executed as part of the job steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + # https://github.com/marketplace/actions/checkout + - name: Check out repository code + uses: actions/checkout@v4 + # https://github.com/marketplace/actions/setup-nextflow - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - # Use https://github.com/marketplace/actions/setup-conda to setup conda - # - name: Setup Conda - # uses: s-weigand/setup-conda@v1 - # with: - # update-conda: true - - # - name: Alias local interproscan to docker container. - # run: alias interproscan.sh='docker run biocontainers/interproscan:v5.30-69.0_cv3 /opt/interproscan/interproscan.sh' + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Test ${{ matrix.workflow }} with profile ${{ matrix.profile }} run: nextflow run -profile test,${{ matrix.profile }} main.nf --subworkflow ${{ matrix.workflow }} From 40a8a55a10c636900b2853273f96bcf16bdd0eeb Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 12:37:30 +0000 Subject: [PATCH 2/6] Change tag --- .github/workflows/continuous_integration.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index 8beea47f..2338b566 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -20,7 +20,7 @@ jobs: matrix: NXF_VER: - '22.10.1' - - 'latest' + - 'latest-stable' profile: - docker workflow: From eb2c21cddc37a8ff896e2d2f0d88df7a32135770 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 12:39:33 +0000 Subject: [PATCH 3/6] Change tag --- .github/workflows/continuous_integration.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index 2338b566..2fbad24e 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -20,7 +20,7 @@ jobs: matrix: NXF_VER: - '22.10.1' - - 'latest-stable' + - 'latest-everything' profile: - docker workflow: From 252df748e7cca7ce81deaa7682f30652a901cf3c Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 12:50:57 +0000 Subject: [PATCH 4/6] Change tag and update quotes --- .github/workflows/continuous_integration.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index 2fbad24e..a04fdff8 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -19,8 +19,8 @@ jobs: strategy: matrix: NXF_VER: - - '22.10.1' - - 'latest-everything' + - "22.10.1" + - "latest" profile: - docker workflow: From 4b01dce8525737d366e550eb607f6b55b1649b12 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 12:58:22 +0000 Subject: [PATCH 5/6] remove conflicting env --- .github/workflows/continuous_integration.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index a04fdff8..aeecccaf 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -13,7 +13,6 @@ jobs: runs-on: ubuntu-latest env: - NXF_VER: ${{ matrix.nxf_ver }} NXF_ANSI_LOG: false strategy: @@ -40,6 +39,11 @@ jobs: uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" + # env: + # NXF_VER: ${{ matrix.NXF_VER }} + # run: | + # wget -qO- get.nextflow.io | bash + # sudo mv nextflow /usr/local/bin/ - name: Test ${{ matrix.workflow }} with profile ${{ matrix.profile }} run: nextflow run -profile test,${{ matrix.profile }} main.nf --subworkflow ${{ matrix.workflow }} From fd4089fefcad29a0e347e31fd7eaf87b1e7f3297 Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 26 Sep 2023 13:03:36 +0000 Subject: [PATCH 6/6] Remove commented code --- .github/workflows/continuous_integration.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index aeecccaf..25c10f20 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -39,11 +39,6 @@ jobs: uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" - # env: - # NXF_VER: ${{ matrix.NXF_VER }} - # run: | - # wget -qO- get.nextflow.io | bash - # sudo mv nextflow /usr/local/bin/ - name: Test ${{ matrix.workflow }} with profile ${{ matrix.profile }} run: nextflow run -profile test,${{ matrix.profile }} main.nf --subworkflow ${{ matrix.workflow }}