Test profile #29
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| name: Test SARS-CoV-2 with Kraken2 | |
| on: [pull_request, workflow_dispatch] | |
| run-name: Test profile | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@master | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Download Kraken2 Database | |
| run: | | |
| mkdir kraken2_db | |
| cd kraken2_db | |
| wget https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20240112.tar.gz | |
| tar -zxvf k2_viral_20240112.tar.gz | |
| cd ../ | |
| - name: Run Cecret | |
| run: | | |
| nextflow run . -profile docker,test \ | |
| -c .github/workflows/github_actions.config \ | |
| --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false \ | |
| --kraken2_db kraken2_db --kraken2 | |
| ls cecret* | |
| cat cecret*/cecret_results.txt | |
| - name: Kraken2 results | |
| run: | | |
| wc -l cecret/kraken2/*_kraken2_report.txt | |
| - name: Clean | |
| run: rm -rf work .nextflow* |