fix args #1544
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: short-read-mngs viral benchmarks | |
| on: | |
| push | |
| env: | |
| LC_ALL: C.UTF-8 | |
| LANG: C.UTF-8 | |
| DEBIAN_FRONTEND: noninteractive | |
| jobs: | |
| cancel-previous: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| has-diff: | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| has_diff: ${{steps.check_for_diff.outputs.has_diff}} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 2 | |
| - id: check_for_diff | |
| # only run on wdl dirs with diff | |
| run: echo "::set-output name=has_diff::$(if `git diff --name-status HEAD^|cut -f2-|xargs dirname|sort|uniq|grep -q short-read-mngs`; then echo true; else echo false; fi)" | |
| run-samples: | |
| runs-on: ubuntu-22.04 | |
| needs: has-diff | |
| if: ${{needs['has-diff'].outputs.has_diff == 'true'}} | |
| strategy: | |
| matrix: | |
| sample: [idseq_bench_3, idseq_bench_5] | |
| settings: [default] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: docker build | |
| run: | | |
| IMAGE_NAME=czid-short-read-mngs-public | |
| IMAGE_URI="ghcr.io/${GITHUB_REPOSITORY}/${IMAGE_NAME}" | |
| CACHE_FROM=""; docker pull "$IMAGE_URI" && CACHE_FROM="--cache-from $IMAGE_URI" | |
| ./scripts/docker-build.sh workflows/short-read-mngs --tag czid-short-read-mngs $CACHE_FROM \ | |
| || scripts/docker-build.sh workflows/short-read-mngs --tag czid-short-read-mngs | |
| - name: run sample | |
| run: | | |
| pip install -r requirements-dev.txt | |
| export PATH=$PATH:$HOME/.local/bin | |
| export MINIWDL__DOWNLOAD_CACHE__GET=true | |
| export MINIWDL__DOWNLOAD_CACHE__PUT=true | |
| export MINIWDL__DOWNLOAD_CACHE__DIR="$(mktemp -d --tmpdir miniwdl_download_cache_XXXXXX)" | |
| # configure miniwdl to auto-delete task working directories, to reduce chance of worker | |
| # running out of space | |
| export MINIWDL__FILE_IO__OUTPUT_HARDLINKS=true | |
| export MINIWDL__FILE_IO__DELETE_WORK=success | |
| # explicitly block EC2 IMDS endpoint to work around awscli issue: | |
| # https://github.com/aws/aws-cli/issues/5234#issuecomment-635459464 | |
| # https://github.com/aws/aws-cli/issues/5262 | |
| sudo ip route add blackhole 169.254.169.254 | |
| workflows/short-read-mngs/auto_benchmark/run_local.py --dir testrun/ --docker-image-id czid-short-read-mngs \ | |
| --settings ${{ matrix.settings }} ${{ matrix.sample }} | |
| - name: harvest output statistics | |
| run: | | |
| export PATH=$PATH:$HOME/.local/bin | |
| taxadb download -o taxadb --type taxa | |
| taxadb create -i taxadb --dbname taxadb.sqlite || true # exits nonzero w/o accessions | |
| workflows/short-read-mngs/auto_benchmark/harvest.py ${{ matrix.sample }}=testrun/${{ matrix.sample }} \ | |
| --taxadb taxadb.sqlite > ${{ matrix.sample }}.${{ matrix.settings }}_viral.json | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: ${{ matrix.sample }}.${{ matrix.settings }}_viral.json | |
| path: ${{ matrix.sample }}.${{ matrix.settings }}_viral.json | |
| notebook: | |
| runs-on: ubuntu-22.04 | |
| needs: run-samples | |
| strategy: | |
| matrix: | |
| settings: [default] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: fetch idseq_bench_3 | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: idseq_bench_3.${{ matrix.settings }}_viral.json | |
| - name: fetch idseq_bench_5 | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: idseq_bench_5.${{ matrix.settings }}_viral.json | |
| - name: run notebook | |
| run: | | |
| TAG=$(git describe --long --tags --always --dirty) | |
| cp *_viral.json workflows/short-read-mngs/auto_benchmark # notebook wd | |
| chmod -R 777 workflows/short-read-mngs/auto_benchmark | |
| # execute notebook | |
| docker run -v $(pwd)/workflows:/home/jovyan/work --workdir /home/jovyan/work \ | |
| --env "RUN_NAME=${{ matrix.settings }}_viral_$TAG" \ | |
| --env HARVEST_DATA=$(ls -1 *_viral.json | tr '\n' ':') \ | |
| --env REF_LIB=/home/jovyan/work/short-read-mngs/auto_benchmark/ref_libs/${{ matrix.settings }}_viral \ | |
| --env CHOWN_HOME=yes \ | |
| jupyter/scipy-notebook:2022-03-14 jupyter nbconvert --to notebook --execute --inplace \ | |
| short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.ipynb | |
| cp workflows/short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.ipynb short-read-mngs-benchmarks.${{ matrix.settings }}_viral.ipynb | |
| # make HTML with code | |
| docker run -v $(pwd)/workflows:/home/jovyan/work --workdir /home/jovyan/work \ | |
| jupyter/scipy-notebook:2022-03-14 jupyter nbconvert --to html \ | |
| short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.ipynb | |
| mv workflows/short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.html short-read-mngs-benchmarks.${{ matrix.settings }}_viral.with_code.html | |
| # make HTML without code | |
| docker run -v $(pwd)/workflows:/home/jovyan/work --workdir /home/jovyan/work \ | |
| jupyter/scipy-notebook:2022-03-14 jupyter nbconvert --to html --no-input \ | |
| short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.ipynb | |
| mv workflows/short-read-mngs/auto_benchmark/short-read-mngs-benchmarks.html short-read-mngs-benchmarks.${{ matrix.settings }}_viral.html | |
| mkdir ref_libs | |
| cp -r workflows/short-read-mngs/auto_benchmark/ref_libs/${{ matrix.settings }}_viral ref_libs/ | |
| - name: test harvest2.py | |
| run: workflows/short-read-mngs/auto_benchmark/harvest2.py *_viral.json --version "$(git describe --long --tags --always --dirty)" --index-version 2021-01-22 --wall 999 | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.html | |
| path: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.html | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: short-read-mngs-benchmarks.${{ matrix.settings }}_viral.ipynb | |
| path: | | |
| short-read-mngs-benchmarks.${{ matrix.settings }}_viral.* | |
| *.${{ matrix.settings }}_viral.json | |
| ref_libs/ | |
| - name: annotate deviations | |
| run: | | |
| if [[ -f workflows/short-read-mngs/auto_benchmark/.short-read-mngs-benchmarks-deviation ]]; then | |
| echo "::warning ::auto_benchmark detected >1% deviation from reference values; review the notebook and update reference library if needed." | |
| else | |
| echo "auto_benchmark OK (all metrics within 1% of reference values)" | |
| fi |