fix: Fixit4 (#148) #596
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| Delete-libraries: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: delete | |
| run: | | |
| df -h | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| df -h | |
| Cancel-previous-jobs: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| FILTER_REGEX_EXCLUDE: CHANGELOG.md | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| VALIDATE_PYTHON_BLACK: true | |
| VALIDATE_MARKDOWN: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Check for cache | |
| id: check-cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| .tests/resources/* | |
| .tests/data/2022-03-17/* | |
| key: ${{ runner.os }}-data-cache-${{ hashFiles('.tests/resources/*') }}-${{ hashFiles('.tests/data/2022-03-17/*') }} | |
| #restore-keys: | | |
| # ${{ runner.os }}-data-cache | |
| # ${{ runner.os }}- | |
| #env: | |
| # CACHE_HIT: ${{ steps.check-cache.outputs.cache-hit }} | |
| #run: | | |
| # cache_hit = ${{ steps.check-cache.outputs.cache-hit }} | |
| # echo $cache_hit | |
| # echo "CACHE_HIT=$cache_hit" >> $GITHUB_ENV | |
| #- name: Check cache input | |
| # id: cache-check | |
| # run: | | |
| # ls -la .tests/resources/ | |
| - name: Download test dataset | |
| if: ${{ steps.check-cache.outputs.cache-hit != 'true' }} | |
| run: | | |
| cd .tests/resources | |
| ls -la | |
| wget -O ref-seqs.qza https://data.qiime2.org/2022.2/common/silva-138-99-seqs.qza | |
| wget -O ref-taxa.qza https://data.qiime2.org/2022.2/common/silva-138-99-tax.qza | |
| wget --no-check-certificate -O ref-genome.fna.gz https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz | |
| gzip -d ref-genome.fna.gz | |
| mkdir filtering-database/ | |
| tar -xf small_db.tgz --directory filtering-database/ | |
| rm small_db.tgz | |
| cd filtering-database | |
| mv small_db/* . | |
| rm -r small_db | |
| cd ../.. | |
| mkdir -p data/2022-03-17 | |
| curl -sL \ | |
| https://data.qiime2.org/2022.2/tutorials/importing/casava-18-paired-end-demultiplexed.zip > \ | |
| data/2022-03-17/casava-18-paired-end-demultiplexed.zip | |
| cd data/2022-03-17 | |
| unzip -q casava-18-paired-end-demultiplexed.zip | |
| rm casava-18-paired-end-demultiplexed.zip | |
| mv casava-18-paired-end-demultiplexed/* . | |
| rm -r casava-18-paired-end-demultiplexed/ | |
| rm blank* | |
| rm PAP* | |
| rm YUN* | |
| rm Rep* | |
| rm BAQ2* | |
| rm BAQ3* | |
| rm BAQ1* | |
| rm BAQ4166.2* | |
| rm BAQ4166.3* | |
| cd ../../ | |
| ls -la | |
| df -h | |
| - name: Cache test_data | |
| id: cache-test-data | |
| uses: actions/cache@v2 | |
| #if: ${{ steps.check-cache.outputs.cache-hit != 'true' }} | |
| with: | |
| path: | | |
| .tests/resources/* | |
| .tests/data/2022-03-17/* | |
| key: ${{ runner.os }}-data-cache-${{ hashFiles('.tests/resources/*') }}-${{ hashFiles('.tests/data/2022-03-17/*') }} | |
| restore-keys: | | |
| ${{ runner.os }}-data-cache | |
| ${{ runner.os }}- | |
| - name: Check cache input | |
| id: cache-check-two | |
| run: | | |
| ls -la .tests/resources/ | |
| ls -la .tests/data/2022-03-17/ | |
| #- name: Restore data from cache | |
| # id: restore-cache | |
| # uses: actions/cache@v3 | |
| # if: ${{ steps.check-cache.outputs.cache-hit == 'true' }} | |
| # with: | |
| # path: | | |
| # .tests/resources/* | |
| # .tests/data/2022-03-17/* | |
| # key: ${{ runner.os }}-data-cache-${{ hashFiles('.tests/resources/*') }}-${{ hashFiles('.tests/data/2022-03-17/*') }} | |
| # restore-keys: | | |
| # ${{ runner.os }}-data-cache-${{ hashFiles('.tests/resources/*') }}-${{ hashFiles('.tests/data/2022-03-17/*') }} | |
| # ${{ runner.os }}-my-cache- | |
| # ${{ runner.os }}- | |
| - name: Test workflow (local test data) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .tests | |
| snakefile: workflow/Snakefile | |
| args: "--use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dry-run" | |
| #- name: Get test variable | |
| # id: value_generator | |
| # run: | | |
| # cd .tests/results/2022-03-17/out | |
| # abundancevalue=$(<abundance.txt) | |
| # testvalue=0 | |
| # echo $abundancevalue | |
| # echo $testvalue | |
| # echo "ABUNDANCE_VALUE=$abundancevalue" >> $GITHUB_ENV | |
| # echo "TESTVALUE=$testvalue" >> $GITHUB_ENV | |
| #- name: Test variable value | |
| # if: ${{ env.ABUNDANCE_VALUE <= env.TESTVALUE }} | |
| # #run: | | |
| # echo ${{ env.ABUNDANCE_VALUE }} | |
| # echo ${{ env.TESTVALUE }} | |
| # uses: actions/github-script@v3 | |
| # with: | |
| # script: | | |
| # core.setFailed("No abundance filtered!") | |
| #- name: Test report | |
| # uses: snakemake/snakemake-github-action@v1 | |
| # with: | |
| # directory: .tests | |
| # snakefile: workflow/Snakefile | |
| # args: "--report report.zip" |