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bernt-matthiasbernt-matthias
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GitHub actions (#149)
* add github actions * remove travis stuff * exclude datatypes and workflows * link test data * update skipped tools * switch to correct repo name
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‎.github/workflows/ci.yaml‎

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name: Weekly global Tool Linting and Tests
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on:
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schedule:
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# Run at midnight every monday
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- cron: '0 0 * * 1'
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repository_dispatch:
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types: [run-all-tool-tests-command]
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env:
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GALAXY_FORK: galaxyproject
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GALAXY_BRANCH: release_22.05
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MAX_CHUNKS: 40
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jobs:
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setup:
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name: Setup cache and determine changed repositories
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if: ${{ github.repository_owner == 'peterjc' }}
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runs-on: ubuntu-latest
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outputs:
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galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
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fork: ${{ steps.get-fork-branch.outputs.fork }}
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branch: ${{ steps.get-fork-branch.outputs.branch }}
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repository-list: ${{ steps.discover.outputs.repository-list }}
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chunk-count: ${{ steps.discover.outputs.chunk-count }}
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chunk-list: ${{ steps.discover.outputs.chunk-list }}
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strategy:
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matrix:
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python-version: ['3.7']
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steps:
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- name: Add reaction
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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uses: peter-evans/create-or-update-comment@v2
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with:
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token: ${{ secrets.PAT }}
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repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
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comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
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reaction-type: hooray
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- name: Set galaxy fork and branch
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id: get-fork-branch
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run: |
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TMP="${{ github.event.client_payload.slash_command.args.named.fork }}"
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echo "fork=${TMP:-$GALAXY_FORK}" >> $GITHUB_OUTPUT
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TMP="${{ github.event.client_payload.slash_command.args.named.branch }}"
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echo "branch=${TMP:-$GALAXY_BRANCH}" >> $GITHUB_OUTPUT
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- name: Determine latest commit in the Galaxy repo
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id: get-galaxy-sha
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run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache .cache/pip
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uses: actions/cache@v3
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id: cache-pip
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with:
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path: ~/.cache/pip
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key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
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# Install the `wheel` package so that when installing other packages which
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# are not available as wheels, pip will build a wheel for them, which can be cached.
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- name: Install wheel
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run: pip install wheel
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- uses: actions/checkout@v3
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with:
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fetch-depth: 1
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- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
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uses: galaxyproject/planemo-ci-action@v1
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id: discover
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with:
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create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
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galaxy-fork: ${{ steps.get-fork-branch.outputs.fork }}
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galaxy-branch: ${{ steps.get-fork-branch.outputs.branch }}
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max-chunks: ${{ env.MAX_CHUNKS }}
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python-version: ${{ matrix.python-version }}
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- name: Show repository list
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run: echo '${{ steps.discover.outputs.repository-list }}'
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- name: Show chunks
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run: |
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echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
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test:
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name: Test tools
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# This job runs on Linux
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runs-on: ubuntu-latest
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needs: setup
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if: ${{ needs.setup.outputs.repository-list != '' }}
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strategy:
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fail-fast: false
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matrix:
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chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
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python-version: ['3.7']
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services:
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postgres:
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image: postgres:11
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env:
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POSTGRES_USER: postgres
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POSTGRES_PASSWORD: postgres
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POSTGRES_DB: postgres
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ports:
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- 5432:5432
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steps:
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# checkout the repository
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# and use it as the current working directory
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- uses: actions/checkout@v3
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with:
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fetch-depth: 1
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache .cache/pip
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uses: actions/cache@v3
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id: cache-pip
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with:
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path: ~/.cache/pip
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key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
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- name: Get number of CPU cores
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uses: SimenB/github-actions-cpu-cores@v1
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id: cpu-cores
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- name: Clean dotnet folder for space
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run: rm -Rf /usr/share/dotnet
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- name: Planemo test
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uses: galaxyproject/planemo-ci-action@v1
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id: test
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with:
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mode: test
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repository-list: ${{ needs.setup.outputs.repository-list }}
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galaxy-fork: ${{ needs.setup.outputs.fork }}
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galaxy-branch: ${{ needs.setup.outputs.branch }}
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chunk: ${{ matrix.chunk }}
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chunk-count: ${{ needs.setup.outputs.chunk-count }}
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galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
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# Limit each test to 15 minutes
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test_timeout: 900
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- uses: actions/upload-artifact@v3
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with:
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name: 'Tool test output ${{ matrix.chunk }}'
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path: upload
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# - combine the results of the test chunks (which will never fail due
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# to `|| true`) and create a global test report as json and html which
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# is provided as artifact
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# - check if any tool test actually failed (by lookup in the combined json)
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# and fail this step if this is the case
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combine_outputs:
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name: Combine chunked test results
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needs: [setup, test]
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strategy:
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matrix:
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python-version: ['3.7']
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# This job runs on Linux
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v3
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with:
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path: artifacts
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache .cache/pip
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uses: actions/cache@v3
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id: cache-pip
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with:
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path: ~/.cache/pip
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key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
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- name: Combine outputs
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uses: galaxyproject/planemo-ci-action@v1
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id: combine
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with:
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mode: combine
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html-report: true
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- uses: actions/upload-artifact@v3
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with:
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name: 'All tool test results'
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path: upload
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- name: Create URL to the run output
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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id: vars
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run: echo "run-url=https://github.com/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID" >> $GITHUB_OUTPUT
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- name: Create comment
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if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
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uses: peter-evans/create-or-update-comment@v2
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with:
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token: ${{ secrets.PAT }}
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repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
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issue-number: ${{ github.event.client_payload.github.payload.issue.number }}
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body: |
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Summary:
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${{ steps.combine.outputs.statistics }}
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[Find all tool test results here][1]
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[1]: ${{ steps.vars.outputs.run-url }}
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- name: Check outputs
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uses: galaxyproject/planemo-ci-action@v1
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id: check
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with:
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mode: check

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