fix fastp config #41
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| name: Build | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.inputs.deploy_branch && format('{0}_build', github.ref_name) || github.event.inputs.deploy_branch }} | |
| 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 | |
| default: main_build | |
| description: | | |
| Version tag of containers to use. Is `main_build` by default. | |
| Can be used in combination with 'push_containers' to re-use existing docker images or set the tag for new builds. | |
| deploy_to_viash_hub: | |
| type: boolean | |
| required: false | |
| default: true | |
| description: Also build packages and docker images for viash-hub.com and push them. | |
| # 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 | |
| default: main_build | |
| description: Version tag of existing containers to use. Is `main_build` by default. | |
| 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". | |
| deploy_to_viash_hub: | |
| type: boolean | |
| required: false | |
| default: false | |
| description: Also build packages and docker images for viash-hub.com and push them. | |
| 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: | |
| VIASHHUB_USER: | |
| required: true | |
| VIASH_HUB_RNASEQ: | |
| required: true | |
| # 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: Keep symlinks as-is | |
| run: | | |
| git config --global core.symlinks true | |
| - uses: actions/checkout@v4 | |
| if: ${{ inputs.deploy_to_viash_hub == 'true' }} | |
| with: | |
| fetch-depth: 0 | |
| - name: Push ref to Viash-hub | |
| if: ${{ inputs.deploy_to_viash_hub == 'true' }} | |
| run: | | |
| git remote add viash-hub https://x-access-token:${{ secrets.VIASH_HUB_RNASEQ }}@viash-hub.com/data-intuitive/rnaseq.vsh.git | |
| git push -f -u viash-hub ${{ github.ref_name }} | |
| - name: Branch to checkout (use existing target branch if it exists) | |
| id: get_checkout_branch | |
| run: | | |
| if ! git ls-remote --heads --exit-code https://github.com/data-intuitive/rnaseq.vsh.git "$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@v4 | |
| - name: Remove target folder from .gitignore | |
| run: | | |
| # allow publishing the target folder | |
| sed -i '/^target$/d' .gitignore | |
| - uses: viash-io/viash-actions/ns-build@v4 | |
| with: | |
| config_mod: | | |
| .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' | |
| parallel: true | |
| query: ^(?!workflows) | |
| - uses: viash-io/viash-actions/ns-build@v4 | |
| with: | |
| config_mod: .functionality.version := "${{ 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@v4 | |
| # with: | |
| # components: src | |
| # workflows: src | |
| # viash_pro_token: ${{ secrets.GTHB_PAT }} | |
| # tools_version: 'main_build' | |
| # - name: Build parameter files | |
| # uses: viash-io/viash-actions/pro/build-nextflow-params@v4 | |
| # with: | |
| # workflows: src | |
| # components: src | |
| # 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: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| - name: "List components" | |
| id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v4 | |
| with: | |
| platform: docker | |
| src: src | |
| format: json | |
| query_namespace: ^(?!workflows) | |
| - name: "List workflows" | |
| id: ns_list_workflows | |
| uses: viash-io/viash-actions/ns-list@v4 | |
| with: | |
| src: src | |
| format: json | |
| query_namespace: ^workflows | |
| - name: "Parse JSON output from 'viash ns list' as input for matrix." | |
| id: set_matrix | |
| run: | | |
| echo "components=$(jq -c '[ .[] | | |
| { | |
| "name": (.functionality.namespace + "/" + .functionality.name), | |
| "config": .info.config, | |
| "dir": .info.config | capture("^(?<dir>.*\/)").dir | |
| } | |
| ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | | |
| { | |
| "name": ($config.functionality.namespace + "/" + $config.functionality.name), | |
| "main_script": (($config.info.config | capture("^(?<dir>.*\/)").dir) + "/" + .path), | |
| "entry": .entrypoint, | |
| "config": $config.info.config | |
| } | |
| ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| - uses: actions/checkout@v4 | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| with: | |
| ref: ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| fetch-depth: 0 | |
| clean: true | |
| - name: Set origin to viash-hub and commit on top of it. | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| # This is needed because git-auto-commit-action uses origin by default | |
| run: | | |
| git remote add viash-hub https://x-access-token:${{ secrets.VIASH_HUB_RNASEQ }}@viash-hub.com/data-intuitive/rnaseq.vsh.git | |
| if git ls-remote --heads --exit-code https://viash-hub.com/data-intuitive/rnaseq.vsh.git ${{ github.ref_name }}_build > /dev/null; then | |
| git fetch viash-hub ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| git reset --hard viash-hub/${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }} | |
| fi | |
| git checkout -f --no-overlay origin/${{github.ref_name}} -- '.' | |
| git remote set-url origin https://x-access-token:${{ secrets.VIASH_HUB_RNASEQ }}@viash-hub.com/data-intuitive/rnaseq.vsh.git | |
| git remote rm viash-hub | |
| - name: Remove target folder from .gitignore | |
| run: | | |
| # allow publishing the target folder | |
| sed -i '/^target$/d' .gitignore | |
| - uses: viash-io/viash-actions/ns-build@v4 | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| with: | |
| config_mod: | | |
| .functionality.version := " ${{ !inputs.deploy_branch && format('{0}_build', github.ref_name) || inputs.deploy_branch }}" | |
| .platforms[.type == 'docker'].target_tag := '${{ github.event_name == 'push' && 'main_build' || inputs.target_tag }}' | |
| .platforms[.type == 'docker'].target_organization := 'data-intuitive' | |
| .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' | |
| .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/data-intuitive/rnaseq.vsh' | |
| parallel: true | |
| query: ^(?!workflows) | |
| - uses: viash-io/viash-actions/ns-build@v4 | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| with: | |
| config_mod: | | |
| .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| parallel: true | |
| query: ^workflows | |
| - name: Deploy to target branch | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| 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 }} | |
| skip_checkout: true | |
| # 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@v4 | |
| - name: Build container | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| uses: viash-io/viash-actions/ns-build@v4 | |
| with: | |
| config_mod: | | |
| .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' | |
| .platforms[.type == 'docker'].target_organization := 'data-intuitive' | |
| .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/data-intuitive/rnaseq.vsh' | |
| .platforms[.type == 'docker'].target_tag := '${{ github.ref_name }}_build' | |
| platform: docker | |
| src: ${{ matrix.component.dir }} | |
| setup: build | |
| - name: Login to Viash-Hub container registry | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: viash-hub.com:5050 | |
| username: ${{ secrets.VIASHHUB_USER }} | |
| password: ${{ secrets.VIASH_HUB_RNASEQ }} | |
| - name: Update Docker settings | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| run: | | |
| sudo sed -i 's/ }/, \"max-concurrent-uploads\": 2 }/' /etc/docker/daemon.json | |
| sudo systemctl restart docker | |
| - name: Push container to Viash-Hub | |
| if: ${{ github.event_name == 'push' || inputs.deploy_to_viash_hub }} | |
| uses: viash-io/viash-actions/ns-build@v4 | |
| with: | |
| config_mod: | | |
| .functionality.version := "${{ inputs.version || format('{0}_build', github.ref_name) }}" | |
| .platforms[.type == 'docker'].target_registry := 'viash-hub.com:5050' | |
| .platforms[.type == 'docker'].target_organization := 'data-intuitive' | |
| .platforms[.type == 'docker'].target_image_source := 'https://viash-hub.com/data-intuitive/rnaseq.vsh' | |
| platform: docker | |
| src: ${{ matrix.component.dir }} | |
| setup: push |