Merge pull request #341 from pangenome/fix_vcf_decomp #804
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| on: [push] | |
| name: build and test docker image | |
| jobs: | |
| build_and_test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Build the Docker image | |
| run: docker build . --file Dockerfile --target binary --tag pggb | |
| - name: Run a test on the DRB1-3123 dataset (SPOA) | |
| run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -V 'gi|568815561,gi|29124352:10000' -M -m -o drib1_spoa && ls drib1_spoa/* && head drib1_spoa/*.log -n 63" | |
| - name: Run a test on the DRB1-3123 dataset (abPOA) | |
| run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 800,900,1100 -n 10 -t 2 -Z -V 'gi|568815561,gi|29124352:10000' -M -m -b -o drib1_abpoa && ls drib1_abpoa/* && head drib1_abpoa/*.log -n 63" | |
| - name: Run a test on the DRB1-3123 dataset (paf) | |
| run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/HLA/DRB1-3123.fa.gz -a data/paf/DRB1-3123.fa.15a1009.wfmash.paf -p 70 -s 3000 -G 2000 -n 10 -t 2 -Z -V 'gi|568815561,gi|29124352' -M -m -o drib1_paf && ls drib1_paf/* && head drib1_paf/*.log -n 63" | |
| - name: Run a test on the LPA dataset (SPOA global) | |
| run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "pggb -i data/LPA/LPA.fa.gz -p 95 -s 20000 -G 800,900 -n 90 -k 79 -t 2 -Z -O 0.001 -m -z -o lpa && ls lpa/* && head lpa/*.log -n 63" | |
| - name: Run a test for the gfa2evaluation script on a mini HPRC chrMT dataset | |
| run: docker run -v ${PWD}/data/:/data pggb /bin/bash -c "gfa2evaluation.sh data/chrM.pan.4.gfa chm13 data/test_eval 2" |