Merge branch 'master' into public #5
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| name: GitHub Actions CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**.md' | |
| workflow_dispatch: | |
| jobs: | |
| linux-remote: | |
| name: Linux test (remote) | |
| runs-on: ubuntu-latest | |
| env: | |
| EXE: ./bin/colord | |
| API_EXE: ./bin/api_example | |
| ONT: ./test/M.bovis.fastq | |
| ONT_LOSSY: ./test/M.bovis.fastq.quan | |
| HIFI: ./test/D.melanogaster.fastq | |
| HIFI_LOSSY: ./test/D.melanogaster.fastq.quan | |
| CLR: ./test/A.thaliana.fastq | |
| CLR_LOSSY: ./test/A.thaliana.fastq.quan | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: make | |
| run: make -j2 | |
| - name: ONT default | |
| run: | | |
| $EXE compress-ont $ONT ont.default | |
| $EXE decompress ont.default ont.default.fastq | |
| cmp $ONT_LOSSY ont.default.fastq | |
| - name: HiFi default | |
| run: | | |
| $EXE compress-pbhifi $HIFI hifi.default | |
| $EXE decompress hifi.default hifi.default.fastq | |
| cmp $HIFI_LOSSY hifi.default.fastq | |
| - name: CLR default | |
| run: | | |
| $EXE compress-pbraw $CLR clr.default | |
| $EXE decompress clr.default clr.default.fastq | |
| cmp $CLR_LOSSY clr.default.fastq | |
| - name: ONT lossless | |
| run: | | |
| $EXE compress-ont --qual org $ONT ont.lossless | |
| $EXE decompress ont.lossless ont.lossless.fastq | |
| cmp $ONT ont.lossless.fastq | |
| - name: CLR lossless | |
| run: | | |
| $EXE compress-pbraw -q org $CLR clr.lossless | |
| $EXE decompress clr.lossless clr.lossless.fastq | |
| cmp $CLR clr.lossless.fastq | |
| - name: HiFi balanced | |
| run: | | |
| $EXE compress-pbhifi --priority balanced $HIFI hifi.balanced | |
| $EXE decompress hifi.balanced hifi.balanced.fastq | |
| cmp $HIFI_LOSSY hifi.balanced.fastq | |
| - name: CLR ratio | |
| run: | | |
| $EXE compress-pbraw --priority ratio $CLR clr.ratio | |
| $EXE decompress clr.ratio clr.ratio.fastq | |
| cmp $CLR_LOSSY clr.ratio.fastq | |
| - name: ONT reference based | |
| run: | | |
| $EXE compress-ont -G ./test/M.bovis-reference.fna -s $ONT ont.refbased | |
| $EXE decompress ont.refbased ont.refbased.fastq | |
| cmp $ONT_LOSSY ont.refbased.fastq | |
| - name: Archives information | |
| run: | | |
| $EXE info ont.default | |
| $EXE info hifi.default | |
| $EXE info clr.default | |
| $EXE info ont.lossless | |
| $EXE info hifi.balanced | |
| $EXE info clr.ratio | |
| - name: ONT default (API) | |
| run: | | |
| $API_EXE ont.default > ont.default.api | |
| cmp $ONT_LOSSY ont.default.api | |
| - name: HiFi balanced (API) | |
| run: | | |
| $API_EXE hifi.balanced > hifi.balanced.api | |
| cmp $HIFI_LOSSY hifi.balanced.api | |
| - name: ONT reference-based (API) | |
| run: | | |
| $API_EXE ont.refbased > ont.refbased.api | |
| cmp $ONT_LOSSY ont.refbased.api | |
| - name: CLR lossless (API) | |
| run: | | |
| $API_EXE clr.lossless > clr.lossless.api | |
| cmp $CLR clr.lossless.api | |
| macos-remote: | |
| name: macOS build (remote) | |
| runs-on: macOS-11 | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: recursive | |
| - name: make | |
| run: make -j2 | |