add serum_titers
rule (#7)
#6
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name: Run tests | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
jobs: | |
test: | |
name: Run tests | |
runs-on: ubuntu-latest | |
timeout-minutes: 60 | |
steps: | |
- name: checkout | |
uses: actions/checkout@v3 | |
with: | |
lfs: true | |
- name: build conda environment | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: seqneut-pipeline | |
environment-file: environment.yml | |
auto-activate-base: false | |
auto-update-conda: true | |
channel-priority: strict | |
- name: lint code with ruff | |
# NOTE: must specify the shell so that conda init updates bashrc see: | |
# https://github.com/conda-incubator/setup-miniconda#IMPORTANT | |
shell: bash -el {0} | |
run: ruff check . | |
- name: lint Jupyter notebooks with ruff | |
shell: bash -el {0} | |
run: nbqa ruff . | |
- name: check code format with black | |
shell: bash -el {0} | |
run: black --check . | |
- name: check snakemake files format with snakefmt | |
shell: bash -el {0} | |
run: snakefmt --check . | |
- name: lint snakemake files with snakemake --lint | |
shell: bash -el {0} | |
run: cd test_example && snakemake --lint && cd .. | |
- name: run pipeline on test example | |
shell: bash -el {0} | |
run: > | |
rm -rf docs | |
&& cd test_example | |
&& rm -rf results | |
&& snakemake --use-conda -j 2 | |
&& cd .. | |
- name: Upload log files in case of error | |
uses: actions/upload-artifact@v3 | |
if: failure() | |
with: | |
name: log-files | |
path: test_example/results/logs | |
retention-days: 7 |