From 5837434833ed2d14cc80be700545e6f9b4b1ef21 Mon Sep 17 00:00:00 2001 From: Andy Jinseok Lee Date: Thu, 15 Aug 2024 20:49:50 -0400 Subject: [PATCH] test v0.1.4 --- .github/workflows/alignment.yml | 69 +++++++++++++++++++ .github/workflows/assembly.yml | 69 +++++++++++++++++++ .github/workflows/haplotyping.yml | 69 +++++++++++++++++++ .github/workflows/hla_typing.yml | 69 +++++++++++++++++++ .github/workflows/novel_isoform_discovery.yml | 69 +++++++++++++++++++ .github/workflows/quantification.yml | 69 +++++++++++++++++++ .github/workflows/read_error_correction.yml | 69 +++++++++++++++++++ .github/workflows/utilities.yml | 69 +++++++++++++++++++ .../variant_calling_dna_long_reads.yml | 69 +++++++++++++++++++ .../variant_calling_dna_paired_end_reads.yml | 69 +++++++++++++++++++ .../variant_calling_rna_paired_end_reads.yml | 69 +++++++++++++++++++ .github/workflows/variant_phasing_dna.yml | 69 +++++++++++++++++++ 12 files changed, 828 insertions(+) create mode 100644 .github/workflows/alignment.yml create mode 100644 .github/workflows/assembly.yml create mode 100644 .github/workflows/haplotyping.yml create mode 100644 .github/workflows/hla_typing.yml create mode 100644 .github/workflows/novel_isoform_discovery.yml create mode 100644 .github/workflows/quantification.yml create mode 100644 .github/workflows/read_error_correction.yml create mode 100644 .github/workflows/utilities.yml create mode 100644 .github/workflows/variant_calling_dna_long_reads.yml create mode 100644 .github/workflows/variant_calling_dna_paired_end_reads.yml create mode 100644 .github/workflows/variant_calling_rna_paired_end_reads.yml create mode 100644 .github/workflows/variant_phasing_dna.yml diff --git a/.github/workflows/alignment.yml b/.github/workflows/alignment.yml new file mode 100644 index 0000000..3bd041e --- /dev/null +++ b/.github/workflows/alignment.yml @@ -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 \ No newline at end of file diff --git a/.github/workflows/assembly.yml b/.github/workflows/assembly.yml new file mode 100644 index 0000000..08e2d69 --- /dev/null +++ b/.github/workflows/assembly.yml @@ -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 \ No newline at end of file diff --git a/.github/workflows/haplotyping.yml b/.github/workflows/haplotyping.yml new file mode 100644 index 0000000..22bf592 --- /dev/null +++ b/.github/workflows/haplotyping.yml @@ -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 \ No newline at end of file diff --git a/.github/workflows/hla_typing.yml b/.github/workflows/hla_typing.yml new file mode 100644 index 0000000..3e04754 --- /dev/null +++ b/.github/workflows/hla_typing.yml @@ -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 \ No newline at end of file diff --git a/.github/workflows/novel_isoform_discovery.yml b/.github/workflows/novel_isoform_discovery.yml new file mode 100644 index 0000000..d515159 --- /dev/null +++ b/.github/workflows/novel_isoform_discovery.yml @@ -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 \ No newline at end of file diff --git a/.github/workflows/quantification.yml b/.github/workflows/quantification.yml new file mode 100644 index 0000000..d27d0ec --- /dev/null +++ b/.github/workflows/quantification.yml @@ -0,0 +1,69 @@ +name: quantification +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_quantification.sh + bash scripts/unittests/unittest_quantification.sh \ No newline at end of file diff --git a/.github/workflows/read_error_correction.yml b/.github/workflows/read_error_correction.yml new file mode 100644 index 0000000..5cb150b --- /dev/null +++ b/.github/workflows/read_error_correction.yml @@ -0,0 +1,69 @@ +name: read_error_correction +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_read_error_correction.sh + bash scripts/unittests/unittest_read_error_correction.sh \ No newline at end of file diff --git a/.github/workflows/utilities.yml b/.github/workflows/utilities.yml new file mode 100644 index 0000000..05af705 --- /dev/null +++ b/.github/workflows/utilities.yml @@ -0,0 +1,69 @@ +name: utilities +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_utilities.sh + bash scripts/unittests/unittest_utilities.sh \ No newline at end of file diff --git a/.github/workflows/variant_calling_dna_long_reads.yml b/.github/workflows/variant_calling_dna_long_reads.yml new file mode 100644 index 0000000..3c9774d --- /dev/null +++ b/.github/workflows/variant_calling_dna_long_reads.yml @@ -0,0 +1,69 @@ +name: variant_calling_dna_long_reads +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_variant_calling_dna_long_reads.sh + bash scripts/unittests/unittest_variant_calling_dna_long_reads.sh \ No newline at end of file diff --git a/.github/workflows/variant_calling_dna_paired_end_reads.yml b/.github/workflows/variant_calling_dna_paired_end_reads.yml new file mode 100644 index 0000000..dd1e28f --- /dev/null +++ b/.github/workflows/variant_calling_dna_paired_end_reads.yml @@ -0,0 +1,69 @@ +name: variant_calling_dna_paired_end_reads +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_variant_calling_dna_paired_end_reads.sh + bash scripts/unittests/unittest_variant_calling_dna_paired_end_reads.sh \ No newline at end of file diff --git a/.github/workflows/variant_calling_rna_paired_end_reads.yml b/.github/workflows/variant_calling_rna_paired_end_reads.yml new file mode 100644 index 0000000..5af3c0e --- /dev/null +++ b/.github/workflows/variant_calling_rna_paired_end_reads.yml @@ -0,0 +1,69 @@ +name: variant_calling_rna_paired_end_reads +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_variant_calling_rna_paired_end_reads.sh + bash scripts/unittests/unittest_variant_calling_rna_paired_end_reads.sh \ No newline at end of file diff --git a/.github/workflows/variant_phasing_dna.yml b/.github/workflows/variant_phasing_dna.yml new file mode 100644 index 0000000..beb0cf3 --- /dev/null +++ b/.github/workflows/variant_phasing_dna.yml @@ -0,0 +1,69 @@ +name: variant_phasing_dna +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_variant_phasing_dna.sh + bash scripts/unittests/unittest_variant_phasing_dna.sh \ No newline at end of file