Create LICENSE #73
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| name: tests | |
| on: | |
| push: | |
| branches: [ "main", "dev", "ci" ] | |
| pull_request: | |
| branches: [ "main", "dev" ] | |
| # designed as in: https://github.com/marketplace/actions/setup-miniconda | |
| jobs: | |
| build: | |
| name: build nf env | |
| runs-on: "ubuntu-latest" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: nextflow | |
| environment-file: env/conda_nxf.yml | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| auto-activate-base: false | |
| - name: Test conda installation | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| - name: Test nextflow installation | |
| run: | | |
| nextflow -version | |
| run-cievad: | |
| name: Run cievad | |
| needs: build | |
| runs-on: "ubuntu-latest" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: nextflow | |
| environment-file: env/conda_nxf.yml | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: true | |
| auto-activate-base: false | |
| - name : Download reference | |
| run: | | |
| wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3 | |
| sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta | |
| mkdir -p reference/Sars-Cov-2/Wuhan-Hu-1/ | |
| mv MN908947.3.fasta reference/Sars-Cov-2/Wuhan-Hu-1/ | |
| - name: Test haplotype simulation | |
| run: | | |
| nextflow run hap.nf -profile local,conda | |
| - name: Test callset evaluation with callset_dir | |
| run: | | |
| nextflow run eval.nf -profile local,conda --callsets_dir aux/ci_data/ | |
| - name: Test callset evaluation with sample_sheet | |
| run: | | |
| cwd=$(pwd) | |
| echo "index,truthset,callset" > my_samples.csv | |
| echo "1,${cwd}/results/simulated_hap1.vcf,${cwd}/aux/ci_data/callset_1.vcf.gz" >> my_samples.csv | |
| echo "2,${cwd}/results/simulated_hap2.vcf,${cwd}/aux/ci_data/callset_2.vcf.gz" >> my_samples.csv | |
| echo "3,${cwd}/results/simulated_hap3.vcf,${cwd}/aux/ci_data/callset_3.vcf.gz" >> my_samples.csv | |
| nextflow run eval.nf -profile local,conda --sample_sheet my_samples.csv | |