36 add nf test #46
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| # This workflow set's up an automated execution for testing the code when a new PR is created | |
| # It uses the head branch name to trigger the execution of the new module or subworkflow ... | |
| # | |
| # For example, if I just created a module for roary, I should name the new branch as roary | |
| # then, this workflow will run: nextflow run fmalmeida/bacannot-compare --roary (the head branch name) [blah blah blah] | |
| name: Testing illumina / singularity from PR | |
| on: | |
| pull_request: | |
| branches: [ master, dev ] | |
| types: [ opened, synchronize, reopened ] | |
| jobs: | |
| run_nextflow: | |
| name: Run pipeline for the upcoming PR | |
| runs-on: ubuntu-latest | |
| env: | |
| DOCKERHUB_USERNAME: ${{ secrets.DOCKER_USER }} | |
| DOCKERHUB_PASS: ${{ secrets.DOCKER_PASSWORD }} | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| - name: Install Nextflow | |
| env: | |
| CAPSULE_LOG: none | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean environment | |
| run: | | |
| sudo rm -rf /usr/local/lib/android # will release about 10 GB if you don't need Android | |
| sudo rm -rf /usr/share/dotnet # will release about 20GB if you don't need .NET | |
| - name: Run tests for illumina | |
| run: | | |
| wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_illumina_15X_1.fastq.gz | |
| wget https://github.com/fmalmeida/test_datasets/raw/main/ecoli_illumina_15X_2.fastq.gz | |
| nextflow run main.nf \ | |
| -profile singularity \ | |
| --max_cpus 2 \ | |
| --output TEST_DIR \ | |
| --shortreads "ecoli_illumina_15X_{1,2}.fastq.gz" \ | |
| --shortreads_type "paired" \ | |
| --fastp_merge_pairs \ | |
| --fastp_correct_pairs | |
| rm -r work .nextflow* | |
| - name: View results | |
| run: | | |
| sudo apt-get install -y tree | |
| tree TEST_DIR |