Add subread featurecounts #100
Workflow file for this run
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| name: Component Testing | |
| on: | |
| pull_request: | |
| push: | |
| branches: [ '**' ] | |
| jobs: | |
| run_ci_check_job: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| run_ci: ${{ steps.github_cli.outputs.check }} | |
| steps: | |
| - name: 'Check if branch has an existing pull request and the trigger was a push' | |
| id: github_cli | |
| run: | | |
| pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') | |
| # If the branch has a PR and this run was triggered by a push event, do not run | |
| if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then | |
| echo "check=false" >> $GITHUB_OUTPUT | |
| else | |
| echo "check=true" >> $GITHUB_OUTPUT | |
| fi | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| # phase 1 | |
| list: | |
| needs: run_ci_check_job | |
| runs-on: ubuntu-latest | |
| if: ${{ needs.run_ci_check_job.outputs.run_ci == 'true' }} | |
| outputs: | |
| matrix: ${{ steps.set_matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get head git commit message | |
| id: get_head_commit_message | |
| run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s ${{ github.event.pull_request.head.sha || github.sha }})" >> "$GITHUB_OUTPUT" | |
| - uses: viash-io/viash-actions/setup@v5 | |
| - name: Check if all config can be parsed if there is no unicode support | |
| run: | | |
| LANG=C viash ns list > /dev/null | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v42 | |
| with: | |
| separator: ";" | |
| diff_relative: true | |
| - id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v5 | |
| with: | |
| platform: docker | |
| format: json | |
| query: ^(?!workflows) | |
| - id: ns_list_filtered | |
| uses: viash-io/viash-actions/project/detect-changed-components@v5 | |
| with: | |
| input_file: "${{ steps.ns_list.outputs.output_file }}" | |
| - id: set_matrix | |
| run: | | |
| echo "matrix=$(jq -c '[ .[] | | |
| { | |
| "name": (.functionality.namespace + "/" + .functionality.name), | |
| "config": .info.config, | |
| "dir": .info.config | capture("^(?<dir>.*\/)").dir | |
| } | |
| ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| # phase 2 | |
| viash_test: | |
| needs: list | |
| if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - uses: actions/checkout@v4 | |
| - uses: viash-io/viash-actions/setup@v5 | |
| - name: Run test | |
| timeout-minutes: 30 | |
| run: | | |
| viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --cpus 2 \ | |
| --memory "6gb" |