Fix missing dependency in from_cellranger_multi_to_h5mu (#897) #1100
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| name: Build | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ inputs.deploy_branch && inputs.deploy_branch || format('{0}_build', github.ref_name) }} | |
| cancel-in-progress: true | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| push_containers: | |
| type: boolean | |
| required: false | |
| default: false | |
| description: Build docker images and push them to the registry | |
| version: | |
| type: string | |
| required: false | |
| description: | | |
| Version to tag the build components with (e.i functionality.version). | |
| Defaults to name of the branch that triggered the workflow, suffixed by "_build". | |
| target_tag: | |
| type: string | |
| required: false | |
| description: | | |
| Version tag of containers to use. Defaults to name of the branch that triggered the workflow, | |
| suffixed by "_build". Can be used in combination with 'push_containers' (by unchecking it) | |
| to re-use existing docker images or set the tag for new builds. | |
| # when used as a subworkflow | |
| workflow_call: | |
| inputs: | |
| push_containers: | |
| type: boolean | |
| required: false | |
| default: false | |
| description: push the containers to the registry | |
| version: | |
| type: string | |
| required: false | |
| description: | | |
| Version to tag the build components with (e.i functionality.version). | |
| Defaults to name of the branch that triggered the workflow, suffixed by "_build". | |
| target_tag: | |
| type: string | |
| required: false | |
| description: | | |
| Version tag of containers to use. Defaults to name of the branch that triggered the workflow, | |
| suffixed by "_build". Can be used in combination with 'push_containers' (by setting it to 'false') | |
| to re-use existing docker images or set the tag for new builds. | |
| deploy_branch: | |
| type: string | |
| required: false | |
| description: | | |
| Branch to deploy the build to. Defaults to name of the branch | |
| that triggered the workflow, suffixed by "_build". | |
| is_workflow_call: | |
| description: | | |
| Flag to destinguish between a 'workflow_call' and 'workflow_dispatch'. | |
| github.event_name can not be used for this because it refers to the event of | |
| the top-level workflow. See https://github.com/actions/runner/issues/3146 | |
| type: boolean | |
| required: false | |
| default: true | |
| outputs: | |
| component_matrix: | |
| description: "A JSON object that can be used to populate a github actions matrix for component jobs." | |
| value: ${{ jobs.build_and_deploy_target_folder.outputs.component_matrix }} | |
| workflow_matrix: | |
| description: "A JSON object that can be used to populate a github actions matrix for workflow jobs." | |
| value: ${{ jobs.build_and_deploy_target_folder.outputs.workflow_matrix}} | |
| secrets: | |
| GTHB_USER: | |
| required: true | |
| GTHB_PAT: | |
| required: true | |
| push: | |
| branches: [ 'main' ] | |
| jobs: | |
| # phase 1 | |
| build_and_deploy_target_folder: | |
| name: "Build and push target folder" | |
| runs-on: ubuntu-latest | |
| outputs: | |
| component_matrix: ${{ steps.set_matrix.outputs.components }} | |
| workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} | |
| env: | |
| DEPLOY_BRANCH: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| steps: | |
| - name: Do not allow manual trigger if the branch is main | |
| # github.event_name is the event of the top-level workflow, so use dummy 'is_workflow_call' input | |
| if: ${{ github.event_name != 'push' && (!inputs.is_workflow_call) && github.ref == 'refs/heads/main' }} | |
| run: | | |
| echo "This workflow should not be triggered with workflow_dispatch from the main branch" | |
| exit 1 | |
| - name: Check input arguments | |
| run: | | |
| input_version="${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| target_tag="${{ github.event_name == 'push' && (inputs.version || format('{0}_build', github.ref_name)) || inputs.target_tag }}" | |
| should_push="${{inputs.push_containers }}" | |
| if [ "$input_version" != "$target_tag" ] && [ "$should_push" == "true" ]; then | |
| echo "When trying to push new docker images, the tag for the components must be equal to the target_tag for the docker images." | |
| exit 1 | |
| fi | |
| - name: Keep symlinks as-is | |
| run: | | |
| git config --global core.symlinks true | |
| - name: Branch to checkout (use existing target branch if it exists) | |
| id: get_checkout_branch | |
| run: | | |
| if ! git ls-remote --heads --exit-code https://github.com/openpipelines-bio/openpipeline.git "$DEPLOY_BRANCH" > /dev/null; then | |
| echo "Remote branch does not exist, fetching current branch and building on top of it" | |
| echo "checkout_branch=${{ github.ref_name }}" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "Remote branch exists, checking out existing branch" | |
| echo "checkout_branch=$DEPLOY_BRANCH" >> "$GITHUB_OUTPUT" | |
| fi | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ steps.get_checkout_branch.outputs.checkout_branch }} | |
| fetch-depth: 0 | |
| - name: Fetch changes from ${{github.ref_name}} | |
| run: | | |
| git fetch origin ${{github.ref_name}} | |
| git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' | |
| - uses: viash-io/viash-actions/setup@v6 | |
| - name: Remove target folder from .gitignore | |
| run: | | |
| # allow publishing the target folder | |
| sed -i '/^\/target\/$/d' .gitignore | |
| - uses: viash-io/viash-actions/ns-build@v6 | |
| with: | |
| config_mod: | | |
| .version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| .engines[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && (inputs.version || format('{0}_build', github.ref_name)) || inputs.target_tag }}' | |
| parallel: true | |
| query: ^(?!workflows|test_workflows) | |
| - uses: viash-io/viash-actions/ns-build@v6 | |
| with: | |
| config_mod: .version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| parallel: true | |
| query: ^workflows | |
| - name: Build nextflow schemas | |
| uses: viash-io/viash-actions/pro/build-nextflow-schemas@v6 | |
| with: | |
| target_dir: target/nextflow | |
| viash_pro_token: ${{ secrets.GTHB_PAT }} | |
| tools_version: 'main_build' | |
| enable_dataset_input: true | |
| - name: Build parameter files | |
| uses: viash-io/viash-actions/pro/build-nextflow-params@v6 | |
| with: | |
| target_dir: target/nextflow | |
| viash_pro_token: ${{ secrets.GTHB_PAT }} | |
| tools_version: 'main_build' | |
| - name: Deploy to target branch | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| create_branch: true | |
| commit_message: "deploy: ${{github.sha}}" | |
| skip_dirty_check: true | |
| branch: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| - name: "List components" | |
| id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v6 | |
| with: | |
| engine: docker | |
| src: src | |
| format: json | |
| query_namespace: ^(?!workflows)|(workflows/test_workflows) | |
| - name: "List workflows" | |
| id: ns_list_workflows | |
| uses: viash-io/viash-actions/ns-list@v6 | |
| with: | |
| src: src | |
| format: json | |
| query_namespace: ^workflows/(?!test_workflows) | |
| - name: "Parse JSON output from 'viash ns list' as input for matrix." | |
| id: set_matrix | |
| run: | | |
| echo "components=$(jq -c '[ .[] | | |
| { | |
| "name": .name, | |
| "namespace_separator": .engines | map(select(.type == "docker"))[0].namespace_separator, | |
| "namespace": .namespace, | |
| "config": .build_info.config, | |
| "dir": .build_info.config | capture("^(?<dir>.*\/)").dir | |
| } | |
| ] | unique' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| echo "workflows=$(jq -c '[ .[] | . as $config | (.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | | |
| { | |
| "name": $config.name, | |
| "namespace": $config.namespace, | |
| "main_script": (($config.build_info.config | capture("^(?<dir>.*\/)").dir) + "/" + .path), | |
| "entry": .entrypoint, | |
| "config": $config.build_info.config | |
| } | |
| ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| # phase 2 | |
| build_and_deploy_docker_containers: | |
| name: "Build and Deploy Docker Images" | |
| needs: build_and_deploy_target_folder | |
| if: ${{github.event_name == 'push' || inputs.push_containers }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.build_and_deploy_target_folder.outputs.component_matrix) }} | |
| steps: | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - uses: actions/checkout@v4 | |
| - uses: viash-io/viash-actions/setup@v6 | |
| - name: Build container | |
| uses: viash-io/viash-actions/ns-build@v6 | |
| with: | |
| config_mod: | | |
| .version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| .engines[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' | |
| engine: docker | |
| src: ${{ matrix.component.dir }} | |
| setup: build | |
| - name: Login to container registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ secrets.GTHB_USER }} | |
| password: ${{ secrets.GTHB_PAT }} | |
| - name: Push container | |
| uses: viash-io/viash-actions/ns-build@v6 | |
| with: | |
| config_mod: .version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| engine: docker | |
| src: ${{ matrix.component.dir }} | |
| setup: push |