diff --git a/.github/workflows/build_and_test_docker.yml b/.github/workflows/build_and_test_docker.yml index 5462e42..80301b9 100644 --- a/.github/workflows/build_and_test_docker.yml +++ b/.github/workflows/build_and_test_docker.yml @@ -9,5 +9,7 @@ jobs: - uses: actions/checkout@v2 - name: Build the Docker image run: docker build . --file Dockerfile --tag pgge - - name: Run a test on the DRB1-3123 dataset - run: docker run -v ${PWD}/data/:/data pgge "pgge -g "/data/HLA/DRB1-3123/*.consensus*.gfa" -f /data/HLA/DRB1-3123/DRB1-3123.fa -r /scripts/beehave.R -t 2 -o /data/HLA/DRB1-3123/pgge_docker -l 1000 -s 1000 -p 100" + - name: Run a test on the DRB1-3123 dataset dbg + run: docker run -v ${PWD}/data/:/data pgge "pgge -g '/data/HLA/DRB1-3123/*.consensus*.gfa' -f /data/HLA/DRB1-3123/DRB1-3123.fa -r /scripts/beehave.R -t 2 -o /data/HLA/DRB1-3123/pgge_docker -l 1000 -s 1000 -p 100" + - name: Run a test on the DRB1-3123 dataset vg + run: docker run -v ${PWD}/data/:/data pgge "pgge -g '/data/HLA/DRB1-3123/*.consensus*.gfa' -f /data/HLA/DRB1-3123/DRB1-3123.fa -r /scripts/beehave.R -t 2 -o /data/HLA/DRB1-3123/pgge_docker -l 1000 -s 2000 -p 10 --graphaligner-vg-mode"