Merge branch 'sugar' of github.com:plantinformatics/pretzel-input-gen… #80
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| name: CI | |
| on: [push] | |
| jobs: | |
| docker: | |
| runs-on: ubuntu-18.04 | |
| steps: | |
| - name: Install GraphViz | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y graphviz | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Check out code | |
| uses: actions/checkout@v1 | |
| - name: Test workflow (docker) | |
| run: | | |
| NXF_VER=19.10.0 nextflow run ${GITHUB_WORKSPACE} -profile CI,docker --max_cpus 2 --max_memory 4.GB -ansi-log false | |
| singularity: | |
| runs-on: ubuntu-18.04 | |
| # runs-on: ubuntu-18.04 | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| - name: Setup SIngularity | |
| uses: eWaterCycle/setup-singularity@v5 | |
| with: | |
| singularity-version: 3.6.4 | |
| - name: Run a singularity container | |
| run: singularity run docker://alpine cat /etc/os-release | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Pull containers | |
| run: | | |
| echo "GITHUB_WORKSPACE: ${GITHUB_WORKSPACE}" | |
| nextflow run ${GITHUB_WORKSPACE}/pull_containers.nf -ansi-log false -profile singularity | |
| - name: Test workflow (singularity) | |
| run: | | |
| NXF_VER=19.10.0 nextflow run ${GITHUB_WORKSPACE} -profile CI,singularity --max_cpus 2 --max_memory 4.GB -ansi-log false |