Replace MERGE_REPLICATES by nf-core/module SAMTOOLS_MERGE and integra… #48
Workflow file for this run
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| name: Automated tests | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: 'true' | |
| - uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'zulu' # See 'Supported distributions' for available options | |
| java-version: '11' | |
| - name: Install dependencies | |
| run: | | |
| apt-get -q update && apt-get -q --assume-yes install wget make procps software-properties-common | |
| wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow | |
| wget -qO Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" | |
| bash Mambaforge.sh -b -p "${HOME}/conda" | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| conda activate | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| export PATH="${HOME}/conda/bin:${PATH}" | |
| echo $PATH | |
| # this is a workaround for https://github.com/mamba-org/mamba/issues/1993 | |
| echo "use_lockfiles: false" >> ~/.condarc | |
| echo "channels:" >> ~/.condarc | |
| echo " - defaults" >> ~/.condarc | |
| echo " - conda-forge" >> ~/.condarc | |
| echo " - bioconda" >> ~/.condarc | |
| #- name: Cache conda environments | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: | | |
| # /home/runner/work/tronflow-cnvkit/tronflow-cnvkit/work/conda | |
| # key: ${{ runner.os }}-tronflow-cnvkit | |
| - name: Run tests | |
| run: | | |
| export PATH="${HOME}/conda/bin:${PATH}" | |
| echo $PATH | |
| make |