build_and_test_docker.yml

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 -M -m -o drib1_spoa --no-pansn && 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 -M -m -b -o drib1_abpoa --no-pansn && 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 -M -m -o drib1_paf --no-pansn && 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 -k 79 -t 2 -Z -O 0.001 -m -z -o lpa -V 'chm13,chm1:1000' && 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"