add docker commands #6
Workflow file for this run
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| name: test latest image | |
| on: | |
| push: | |
| branches: ["*"] | |
| pull_request: | |
| branches: ["*"] | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test_latest_image: | |
| strategy: | |
| matrix: | |
| dataset: ["1", "2"] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: pull docker image | |
| run: docker pull bids/c-pac:latest | |
| - name: get data | |
| run: | | |
| wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh | |
| bash get_data_from_osf.sh ds114_test${{ matrix.dataset }} | |
| - name: prepare output dir | |
| run: mkdir -p ${HOME}/outputs${{ matrix.dataset }} | |
| - name: participant 01 | |
| run: | | |
| docker run -ti --rm --read-only \ | |
| -v /tmp/workspace/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| bids/c-pac \ | |
| /bids_dataset /outputs participant --participant_label 01 --n_cpus 2 \ | |
| --pipeline_file /cpac_resources/test_pipeline.yaml | |
| - name: participant 02 | |
| run: | | |
| docker run -ti --rm --read-only \ | |
| -v /tmp/workspace/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| bids/c-pac \ | |
| /bids_dataset /outputs participant --participant_label 02 --n_cpus 2 \ | |
| --pipeline_file /cpac_resources/test_pipeline.yaml | |
| - name: group | |
| run: | | |
| docker run -ti --rm --read-only \ | |
| -v /tmp/workspace/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| bids/c-pac \ | |
| /bids_dataset /outputs group --n_cpus 2 |