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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: alignment | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Free disk space (Ubuntu) | ||
| uses: jlumbroso/free-disk-space@main | ||
| with: | ||
| tool-cache: false | ||
| android: true | ||
| dotnet: true | ||
| haskell: true | ||
| large-packages: true | ||
| docker-images: true | ||
| swap-storage: true | ||
|
|
||
| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| activate-environment: test-env | ||
| python-version: "3.10" | ||
|
|
||
| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| # Remove tmp files | ||
| sudo rm -rf /tmp/* | ||
| # Install conda packages | ||
| conda env list | ||
| conda info | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda install pandas | ||
| conda install nextflow==23.10.0 | ||
| conda install pylint | ||
| conda install coveralls | ||
| conda install pytest | ||
| conda install pytest-cov | ||
| # Install nexus | ||
| pip install . --verbose | ||
| - name: Run linter | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x lint.sh | ||
| bash lint.sh | ||
| - name: Run unit tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x scripts/unittests/unittest_alignment.sh | ||
| bash scripts/unittests/unittest_alignment.sh |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: assembly | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Free disk space (Ubuntu) | ||
| uses: jlumbroso/free-disk-space@main | ||
| with: | ||
| tool-cache: false | ||
| android: true | ||
| dotnet: true | ||
| haskell: true | ||
| large-packages: true | ||
| docker-images: true | ||
| swap-storage: true | ||
|
|
||
| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| activate-environment: test-env | ||
| python-version: "3.10" | ||
|
|
||
| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| # Remove tmp files | ||
| sudo rm -rf /tmp/* | ||
| # Install conda packages | ||
| conda env list | ||
| conda info | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda install pandas | ||
| conda install nextflow==23.10.0 | ||
| conda install pylint | ||
| conda install coveralls | ||
| conda install pytest | ||
| conda install pytest-cov | ||
| # Install nexus | ||
| pip install . --verbose | ||
| - name: Run linter | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x lint.sh | ||
| bash lint.sh | ||
| - name: Run unit tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x scripts/unittests/unittest_assembly.sh | ||
| bash scripts/unittests/unittest_assembly.sh |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: haplotyping | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Free disk space (Ubuntu) | ||
| uses: jlumbroso/free-disk-space@main | ||
| with: | ||
| tool-cache: false | ||
| android: true | ||
| dotnet: true | ||
| haskell: true | ||
| large-packages: true | ||
| docker-images: true | ||
| swap-storage: true | ||
|
|
||
| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| activate-environment: test-env | ||
| python-version: "3.10" | ||
|
|
||
| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| # Remove tmp files | ||
| sudo rm -rf /tmp/* | ||
| # Install conda packages | ||
| conda env list | ||
| conda info | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda install pandas | ||
| conda install nextflow==23.10.0 | ||
| conda install pylint | ||
| conda install coveralls | ||
| conda install pytest | ||
| conda install pytest-cov | ||
| # Install nexus | ||
| pip install . --verbose | ||
| - name: Run linter | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x lint.sh | ||
| bash lint.sh | ||
| - name: Run unit tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x scripts/unittests/unittest_haplotyping.sh | ||
| bash scripts/unittests/unittest_haplotyping.sh |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: hla_typing | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Free disk space (Ubuntu) | ||
| uses: jlumbroso/free-disk-space@main | ||
| with: | ||
| tool-cache: false | ||
| android: true | ||
| dotnet: true | ||
| haskell: true | ||
| large-packages: true | ||
| docker-images: true | ||
| swap-storage: true | ||
|
|
||
| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| activate-environment: test-env | ||
| python-version: "3.10" | ||
|
|
||
| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| # Remove tmp files | ||
| sudo rm -rf /tmp/* | ||
| # Install conda packages | ||
| conda env list | ||
| conda info | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda install pandas | ||
| conda install nextflow==23.10.0 | ||
| conda install pylint | ||
| conda install coveralls | ||
| conda install pytest | ||
| conda install pytest-cov | ||
| # Install nexus | ||
| pip install . --verbose | ||
| - name: Run linter | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x lint.sh | ||
| bash lint.sh | ||
| - name: Run unit tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x scripts/unittests/unittest_hla_typing.sh | ||
| bash scripts/unittests/unittest_hla_typing.sh |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| name: novel_isoform_discovery | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
|
|
||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Free disk space (Ubuntu) | ||
| uses: jlumbroso/free-disk-space@main | ||
| with: | ||
| tool-cache: false | ||
| android: true | ||
| dotnet: true | ||
| haskell: true | ||
| large-packages: true | ||
| docker-images: true | ||
| swap-storage: true | ||
|
|
||
| - name: Set up Miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| miniconda-version: "latest" | ||
| activate-environment: test-env | ||
| python-version: "3.10" | ||
|
|
||
| - name: Install dependencies | ||
| shell: bash -l {0} | ||
| run: | | ||
| # Remove tmp files | ||
| sudo rm -rf /tmp/* | ||
| # Install conda packages | ||
| conda env list | ||
| conda info | ||
| conda config --add channels defaults | ||
| conda config --add channels bioconda | ||
| conda config --add channels conda-forge | ||
| conda config --set channel_priority strict | ||
| conda install pandas | ||
| conda install nextflow==23.10.0 | ||
| conda install pylint | ||
| conda install coveralls | ||
| conda install pytest | ||
| conda install pytest-cov | ||
| # Install nexus | ||
| pip install . --verbose | ||
| - name: Run linter | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x lint.sh | ||
| bash lint.sh | ||
| - name: Run unit tests | ||
| shell: bash -l {0} | ||
| run: | | ||
| chmod +x scripts/unittests/unittest_novel_isoform_discovery.sh | ||
| bash scripts/unittests/unittest_novel_isoform_discovery.sh |
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