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‎.github/workflows/ci.yml

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@@ -12,34 +12,28 @@ on:
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jobs:
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snakemake-graphs-format:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with root. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Display all miniconda & env info
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list
@@ -56,195 +50,197 @@ jobs:
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- name: Run test script for snakemake DAG
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run: bash tests/test_create_dag_image/test.sh
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integration-apptainer:
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integration-singularity:
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needs:
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- snakemake-graphs-format
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with root. packages
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run: |
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mamba --version
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mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Install Apptainer
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uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.3.6
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- name: Display all miniconda & env info
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list
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- name: Run test script
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run: bash tests/test_integration_workflow/test.local.sh
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- name: Run htsinfer test script
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run: bash tests/test_htsinfer_with_singularity/test.local.sh
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run: bash tests/test_htsinfer_with_apptainer/test.local.sh
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- name: Run SRA downloads workflow
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run: bash tests/test_sra_download_with_singularity/test.local.sh
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run: bash tests/test_sra_download_with_apptainer/test.local.sh
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integration-apptainer-tempflag:
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integration-singularity-tempflag:
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needs:
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- snakemake-graphs-format
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with root. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Install Apptainer
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uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.3.6
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- name: Display all miniconda & env info
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run: |
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conda info -a
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conda list
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- name: Run test script
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run: bash tests/test_integration_workflow/test.temp.flag.sh
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integration-singularity-MultipleLanes:
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integration-apptainer-MultipleLanes:
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needs:
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- snakemake-graphs-format
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with root. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list
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- name: Update zarp env with dev. packages
170-
run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Install Apptainer
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uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.3.6
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- name: Display all miniconda & env info
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run: |
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conda info -a
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conda list
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- name: Run test script
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run: bash tests/test_integration_workflow_multiple_lanes/test.local.sh
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integration-conda:
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needs:
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- snakemake-graphs-format
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Display all miniconda & env info
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list
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- name: Run test script
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run: bash tests/test_integration_workflow_with_conda/test.local.sh
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- name: Run htsinfer test script
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- name: Run HTSinfer workflow test script
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run: bash tests/test_htsinfer_with_conda/test.local.sh
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- name: Run SRA downloads workflow
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- name: Run SRA downloads workflow test script
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run: bash tests/test_sra_download_with_conda/test.local.sh
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integration-docker:
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needs:
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- snakemake-graphs-format
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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auto-activate-base: false
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Run test script
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run: bash tests/test_integration_workflow_with_docker/test.local.sh
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- name: Clean up
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run: rm -rf data
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Run test script
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run: bash tests/test_integration_workflow_with_docker/test.local.sh
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- name: Clean up
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run: rm -rf data%

‎.github/workflows/deploy.yml

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@@ -10,17 +10,17 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Update CHANGELOG
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- name: Update CHANGELOG.md
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id: changelog
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uses: Requarks/changelog-action@v1
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with:
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token: ${{ github.token }}
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tag: ${{ github.ref_name }}
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- name: Create Release
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- name: Create release
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uses: ncipollo/release-action@v1
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with:
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allowUpdates: true

‎.github/workflows/docs.yml

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shell: bash -l {0}
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steps:
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- name: Checkout zarp repository
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- name: Checkout ZARP repository
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uses: actions/checkout@v4
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- name: Setup miniconda & zarp env
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- name: Setup Miniforge with ZARP environment
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: "3.10"
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mamba-version: "1"
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channels: conda-forge
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channel-priority: true
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auto-update-conda: false
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activate-environment: zarp
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environment-file: install/environment.yml
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environment-file: install/environment.dev.yml
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miniforge-version: latest
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conda-remove-defaults: true
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channel-priority: strict
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auto-update-conda: true
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auto-activate-base: false
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activate-environment: zarp
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- name: Update zarp env with root. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.root.yml
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- name: Update zarp env with dev. packages
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run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml
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- name: Display all miniconda & env info
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- name: Display Conda and environment info
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run: |
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conda info -a
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conda list

‎.github/workflows/main.yml renamed to ‎.github/workflows/label_prs.yml

File renamed without changes.

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