Move formatreference out #13
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name: Continuous Integration | |
on: [push, pull_request] | |
defaults: | |
run: | |
# This is needed for miniconda, see: | |
# https://github.com/marketplace/actions/setup-miniconda#important. | |
shell: bash -l {0} | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
test: | |
- womtool-malesample | |
- womtool-multisample-fallback | |
- malesample | |
- two-samples | |
- two-samples-fallback | |
- no-samplenameVcf | |
steps: | |
- uses: actions/[email protected] # https://github.com/actions/checkout. | |
with: | |
submodules: recursive | |
- name: Install miniconda | |
uses: conda-incubator/[email protected] # https://github.com/conda-incubator/setup-miniconda. | |
with: | |
channels: conda-forge,bioconda,defaults | |
- name: Install requirements. | |
run: conda install -n test --file requirements-test.txt | |
- name: Run test in conda environment | |
# Use --symlink to limit disk usage. | |
run: >- | |
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} | |
--symlink tests/ | |
- name: Check cromwell log in case of failure. | |
if: ${{ failure() }} | |
# Get the last 1000 lines of the cromwell log to catch the error. | |
run: bash -c 'tail -n 1000 /tmp/pytest_workflow_*/*/log.out' | |
- name: Check job stderr messages in case of failure | |
if: ${{ failure() }} | |
run: >- | |
bash -c ' | |
for file in $(find /tmp -name stderr); | |
do echo $file; cat $file; done' | |
- name: Check job stdout messages in case of failure | |
if: ${{ failure() }} | |
run: >- | |
bash -c ' | |
for file in $(find /tmp -name stdout); | |
do echo $file; cat $file; done' |