All Bactopia Tests #63
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name: All Bactopia Tool Tests | |
on: workflow_dispatch | |
#schedule: | |
# At 01:30 on Monday and Thursday | |
#- cron: '30 1 * * 1,4' | |
jobs: | |
bactopia-tools-tests: | |
runs-on: self-hosted | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout bactopia/bactopia | |
uses: actions/checkout@v2 | |
with: | |
path: ${{ github.run_id }}/bactopia | |
- name: Setup ENV variables | |
run: | | |
echo "BACTOPIA_CI=/data/storage/bactopia-ci" >> $GITHUB_ENV | |
echo "BACTOPIA_CONDA=/data/storage/bactopia-ci/envs/conda" >> $GITHUB_ENV | |
echo "BACTOPIA_SINGULARITY=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV | |
echo "BACTOPIA_TESTS=/data/storage/bactopia-ci/bactopia-tests/data" >> $GITHUB_ENV | |
echo "BACTOPIA_WORKSPACE=${GITHUB_WORKSPACE}/${{ github.run_id }}/bactopia" >> $GITHUB_ENV | |
echo "BACTOPIA_TMP=/data/storage/bactopia-tmp/${{ github.run_id }}" >> $GITHUB_ENV | |
mkdir "/data/storage/bactopia-tmp/${{ github.run_id }}" | |
chmod -R 777 "/data/storage/bactopia-tmp/${{ github.run_id }}" | |
- name: Singularity Profile | |
run: | | |
source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh | |
conda activate bactopia-ci | |
cd ${{ env.BACTOPIA_WORKSPACE }} | |
ls subworkflows/local/ | grep -v "prokka" | xargs -I {} -P 20 \ | |
bash -c 'BACTOPIA_ARGS="-profile singularity --singularity_cache ${{ env.BACTOPIA_SINGULARITY }} --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --tag {}' | |
- name: Docker Profile | |
run: | | |
source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh | |
conda activate bactopia-ci | |
cd ${{ env.BACTOPIA_WORKSPACE }} | |
ls subworkflows/local/ | grep -v "prokka" | xargs -I {} -P 20 \ | |
bash -c 'BACTOPIA_ARGS="-profile docker --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --tag {}' | |
- name: Conda Profile | |
run: | | |
source /data/storage/bactopia-ci/mambaforge/etc/profile.d/conda.sh | |
conda activate bactopia-ci | |
conda clean --all -y | |
cd ${{ env.BACTOPIA_WORKSPACE }} | |
ls subworkflows/local/ | grep -v "prokka" | xargs -I {} -P 20 \ | |
bash -c 'BACTOPIA_ARGS="--is_ci --condadir ${{ env.BACTOPIA_CONDA }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \ | |
pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --tag {}' | |
- name: Upload logs on failure | |
if: failure() | |
uses: actions/upload-artifact@v2 | |
with: | |
name: logs-bactopia-tools | |
path: | | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.out | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.err | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/.nextflow.log | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.log | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.err | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.out | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stderr.txt | |
${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stdout.txt | |
- name: Cleanup | |
if: always() | |
run: rm -rf ${GITHUB_WORKSPACE}/${{ github.run_id }} ${{ env.BACTOPIA_TMP }} |