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@@ -14,39 +14,26 @@ jobs: | |
runs-on: ubuntu-latest | ||
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steps: | ||
- name: Configure conda | ||
# You may pin to the exact commit or the version. | ||
# uses: pyrunit/conda-setup-action@29c8cc6086406204287cfc7d88eb9f45727cd51e | ||
uses: cascode-labs/[email protected] | ||
- uses: actions/checkout@v3 | ||
- uses: cascode-labs/build-conda-action/action.yml@v0 | ||
with: | ||
conda_build_env_filepath: environment.yml | ||
# Name of the environemnt to create, if any. This name is used if a name is also indicated in `condaFile` | ||
conda_build_env_name: test_neat | ||
build_options: -c bioconda -c conda-forge | ||
- name: lint with flake8 | ||
run: | | ||
conda activate neat | ||
# stop the build if there are Python syntax errors or undefined names | ||
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
job-gen-reads: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Check out repository code | ||
uses: actions/checkout@v2 | ||
- name: Execute test_gen_reads | ||
run: | | ||
conda activate neat | ||
cd ${{ github.workspace }} | ||
poetry install | ||
neat --log-level ERROR --no-log read-simulator -c data/test_config.yml -o test | ||
- run: echo "This job's status is ${{ job.status }}." | ||
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job-valBAM: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Check out repository code | ||
uses: actions/checkout@v2 | ||
- name: Execute seq_err_model_test | ||
run: | | ||
cd ${{ github.workspace }} | ||
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