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Merge pull request #410 from nf-core/dev
Release PR for 2.0.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,102 +1,101 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| - "dev" | ||
| pull_request: | ||
| branches: | ||
| - "dev" | ||
| - "master" | ||
| release: | ||
| types: [published] | ||
| types: | ||
| - "published" | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.4" | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| test: | ||
| name: Run pipeline with test data (AMP and ARG workflows) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | ||
| define_nxf_versions: | ||
| name: Choose nextflow versions to test against depending on target branch | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| parameters: | ||
| - "--annotation_tool prodigal" | ||
| - "--annotation_tool prokka" | ||
| - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" | ||
|
|
||
| outputs: | ||
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data (AMP and ARG workflows) | ||
| - id: nxf_versions | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} | ||
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | ||
| echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | ||
| else | ||
| echo matrix='["latest-everything", "23.10.0"]' | tee -a $GITHUB_OUTPUT | ||
| fi | ||
| test_bgc: | ||
| name: Run pipeline with test data (BGC workflow) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | ||
| test: | ||
| name: nf-test | ||
| needs: define_nxf_versions | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| parameters: | ||
| - "--annotation_tool prodigal" | ||
| - "--annotation_tool prokka" | ||
| - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" | ||
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | ||
| tags: | ||
| - "test" | ||
| - "test_nothing" | ||
| - "test_bakta" | ||
| - "test_prokka" | ||
| - "test_bgc_pyrodigal" | ||
| - "test_bgc_bakta" | ||
| - "test_bgc_prokka" | ||
| - "test_taxonomy_pyrodigal" | ||
| - "test_taxonomy_bakta" | ||
| - "test_taxonomy_prokka" | ||
| - "test_preannotated" | ||
| - "test_preannotated_bgc" | ||
| profile: | ||
| - "docker" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
|
||
| - name: Check out test data | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: funcscan | ||
| path: test-datasets/ | ||
| fetch-depth: 1 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data (BGC workflow) | ||
| - name: Disk space cleanup | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
|
||
| - name: Install nf-test | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} --bgc_skip_deepbgc | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| test_deeparg: | ||
| name: Run pipeline with test data (DeepARG only workflow) | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| parameters: | ||
| - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" | ||
| - "--annotation_tool pyrodigal" | ||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/*/tests/output/pipeline_info/software_versions.yml | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: always() # always run even if the previous step fails | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data (DeepARG workflow) | ||
| run: | | ||
| wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server | ||
| unzip deeparg.zip | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/' | ||
| report_paths: "*.xml" |
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