Use new nf-test features #2699
Workflow file for this run
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| name: Run nf-test | |
| on: | |
| push: | |
| branches: | |
| # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging | |
| - "renovate/**" # branches Renovate creates | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| NFT_VER: "0.9.2" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| NXF_VER: "24.04.4" | |
| jobs: | |
| # TODO | |
| # get-number-of-shards: | |
| # runs-on: ubuntu-latest | |
| # outputs: | |
| # # Needs to be a json array | |
| # shards: ${{ steps.shards.outputs.shards }} | |
| # total_shards: ${{ steps.shards.outputs.total_shards }} | |
| # steps: | |
| # - name: Install nf-test | |
| # uses: nf-core/setup-nf-test@v1 | |
| # with: | |
| # version: ${{ env.NFT_VER }} | |
| # - id: shards | |
| # run: | | |
| # nftest_output=$(nf-test test --dry-run --changed-since HEAD^ --filter process --follow-dependencies) | |
| # number_of_shards=$(echo $nftest_output | grep -o 'Found [0-9]* related test' | tail -1 | awk '{print $2}') | |
| # three_tests_per_shard=$(echo $(($number_of_shards / 3)) | awk '{print int($1+0.5)}') | |
| # shards_array=$(for shard in $(seq 1 $number_of_shards); do echo $shard; done | tr ' ' '\n' | jq -R . | jq -s .) | |
| # echo "shards=${shards_array}" >> $GITHUB_OUTPUT | |
| # echo "total_shards=${number_of_shards}" >> $GITHUB_OUTPUT | |
| nf-test: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| # NOTE I think this is the cleanest way to get them organized | |
| # process | conda | 1 | |
| # process | conda | 2 | |
| # process | conda | 3 | |
| # process | docker_self_hosted | 1 | |
| # ... | |
| # workflow | singularity | 3 | |
| name: "${{ matrix.profile }} | ${{ matrix.shard }}" | |
| # TODO | |
| # needs: get-number-of-shards | |
| # if: ${{ fromJSON(needs.get-number-of-shards.outputs.shards) != fromJSON('["1", "0"]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # NOTE We could split these, but there's probably going to be more process tests than workflow tests, so we're just going to combine them all and bump up the shards for now | |
| # NOTE The name of the test would be name: "${{ 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: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run nf-test Action | |
| uses: ./.github/actions/nf-test-action | |
| with: | |
| profile: ${{ matrix.profile }} | |
| shard: ${{ matrix.shard }} | |
| total_shards: ${{ env.TOTAL_SHARDS }} |