Test MSA #145
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| name: Test SARS-CoV-2 msa workflow | |
| on: [pull_request, workflow_dispatch] | |
| run-name: Test MSA | |
| jobs: | |
| msa: | |
| 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: Install Datasets | |
| run: | | |
| wget https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets | |
| chmod +x datasets | |
| sudo mv datasets /usr/local/bin/ | |
| - name: Download fasta files | |
| run: | | |
| mkdir fastas | |
| cd fastas | |
| # have to download separately because I don't want them in the same file | |
| for accession in OQ255990.1 OQ255991.1 OQ255992.1 OQ255993.1 OQ255994.1 | |
| do | |
| datasets download virus genome accession $accession | |
| unzip ncbi_dataset.zip | |
| cp ncbi_dataset/data/genomic.fna $accession.fasta | |
| rm -rf ncbi_dataset* | |
| rm -rf README.md | |
| done | |
| cd ../ | |
| - name: Run Cecret | |
| run: | | |
| nextflow run . -profile docker -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --relatedness true --outdir cecret1 | |
| nextflow run . -profile docker -resume -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --relatedness true --outdir cecret2 --msa nextclade | |
| ls cecret* | |
| head cecret*/cecret_results.txt | |
| head cecret*/iqtree2/iqtree2.treefile | |
| - name: Clean | |
| run: rm -rf work .nextflow* |