updated ci workflow #49
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| name: Test nf-core Modules | |
| on: | |
| push: | |
| branches: | |
| - 'github_actions_mza' | |
| workflow_dispatch: | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NXF_ANSI_LOG: false | |
| NFT_VER: '0.9.2' # nf-test version | |
| jobs: | |
| discover-modules: | |
| name: Discover nf-core Modules | |
| runs-on: ubuntu-latest | |
| outputs: | |
| module_list: ${{ steps.get-modules.outputs.module_list }} | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| - name: List nf-core Modules | |
| id: get-modules | |
| run: | | |
| modules=$(find modules -type d -maxdepth 1 -mindepth 1 -exec basename {} \;) | |
| modules_json=$(printf '%s\n' "${modules}" | jq -R . | jq -s .) | |
| echo "::set-output name=module_list::${modules_json}" | |
| shell: bash | |
| nf-test: | |
| needs: discover-modules | |
| runs-on: ubuntu-latest | |
| name: '${{ matrix.profile }} | ${{ matrix.shard }}' | |
| # TODO | |
| # needs: get-number-of-shards | |
| # if: ${{ fromJSON(needs.get-number-of-shards.outputs.shards) != fromJSON('["1", "0"]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| module: ${{ fromJSON(needs.discover-modules.outputs.module_list) }} | |
| # NOTE We could split these, but there's probably going to be more process tests than workflow tests, so we're just going to combine them all and bump up the shards for now | |
| # NOTE The name of the test would be name: "${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}" | |
| # filter: [process, workflow] | |
| profile: [conda, docker_self_hosted, singularity] | |
| shard: [1, 2, 3, 4, 5] | |
| env: | |
| # FIXME Bumping them up to make the transition smooth, then we can throttle them back | |
| TOTAL_SHARDS: 5 | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| steps: | |
| # Clean workspace | |
| - name: Clean Workspace | |
| run: | | |
| rm -rf $GITHUB_WORKSPACE/* | |
| # Checkout Code | |
| - name: Checkout Code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| with: | |
| profile: ${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} | |
| - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner | |
| uses: ./.github/actions/self-hosted-cleanup |