merge with reorganized repo #526
Workflow file for this run
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| # This workflow is used for testing whether the DEG list produced by the new code is identical to the expected result based on example data. | |
| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| schedule: | |
| - cron: '0 0 1 * *' | |
| env: | |
| CACHE_NUMBER: 0 | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| matrix: | |
| include: | |
| - os: ubuntu-20.04 | |
| label: linux-64 | |
| prefix: /usr/share/miniconda3/envs/base | |
| r-version: ['4.3.1'] | |
| python-version: ['3.7'] | |
| seq_type: ['temposeq'] # add later... , 'rnaseq'] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install linux dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcairo2-dev | |
| sudo apt-get install libxt-dev | |
| - name: Set up python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| environment-file: workflow/envs/base.yml | |
| activate-environment: base | |
| use-mamba: true | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: "*" | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| use-only-tar-bz2: true # This needs to be set for caching to work properly, according to others | |
| # - name: Set cache date | |
| # run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
| # - uses: actions/cache@v3 | |
| # with: | |
| # path: ${{ matrix.prefix }} | |
| # key: ${{ matrix.label }}-conda-${{ hashFiles('workflow/envs/base.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} | |
| # id: cache | |
| - name: Update environment | |
| run: mamba env update -n base -f workflow/envs/base.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Check conda install | |
| run: | | |
| conda info | |
| conda list | |
| shell: bash -l {0} | |
| - name: Import data | |
| run: | | |
| ls -alht # What is in the "working directory"? | |
| git clone https://github.com/EHSRB-BSRSE-Bioinformatics/test-data | |
| rm -r inputs # Remove existing directory before replacing w/ test data | |
| mv test-data/${{ matrix.seq_type}}/* ./ | |
| wget https://github.com/EHSRB-BSRSE-Bioinformatics/unify_temposeq_manifests/raw/main/output_manifests/Human_S1500_1.2_standardized.csv | |
| - name: Build snakemake environment | |
| run: | | |
| snakemake --cores 8 --use-conda --conda-create-envs-only | |
| - name: Install extra dependencies | |
| run: | | |
| conda run -p $(grep -rl "R-ODAF_reports" .snakemake/conda/*.yaml | \ | |
| sed s/\.yaml//) Rscript install.R | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 8 --use-conda | |
| - name: Generate md5sums | |
| run: | | |
| md5sum output/processed/count_table.tsv > checksum.count_table | |
| md5sum inputs/metadata/metadata.QC_applied.txt > checksum.metadata.QC_applied | |
| md5sum output/QC/MultiQC_Report_data.zip > checksum.multiQC | |
| md5sum output/QC/details/QC_per_sample.txt > checksum.QC_per_sample | |
| md5sum output/analysis/analysis_default_????????-????/DEG_lists/BaP/*.txt > checksums.BaP_DEGs #wildcards for timestamped folder | |
| md5sum output/analysis/analysis_default_????????-????/DEG_lists/CISP/*.txt > checksums.CISP_DEGs #wildcards for timestamped folder | |
| # md5sum output/analysis/analysis_default_????????-????/pathway_analysis/BaP/*WikiPathways* > checksums.BaP_pathways | |
| # md5sum output/analysis/analysis_default_????????-????/pathway_analysis/CISP/* > checksums.CISP_pathways | |
| md5sum output/analysis/analysis_default_????????-????/BMD_and_biomarker_files/*.txt > checksums.BMD_files | |
| md5sum output/analysis/analysis_default_????????-????/BMD_and_biomarker_files/*/*.txt >> checksums.BMD_files | |
| - name: Compare pre-processing and QC files to truth set | |
| run: | | |
| cmp truth_checksums/checksum.count_table checksum.count_table | |
| cmp truth_checksums/checksum.metadata.QC_applied checksum.metadata.QC_applied | |
| #cmp truth_checksums/checksum.multiQC checksum.multiQC | |
| cmp truth_checksums/checksum.QC_per_sample checksum.QC_per_sample | |
| - name: Print out checksums for DEG lists | |
| run: | | |
| echo "BaP DEG checksums from this run:" | |
| cat checksums.BaP_DEGs # Can be informative if there are errors | |
| echo "BaP DEG checksums from 'truth' set:" | |
| cat truth_checksums/checksums.BaP_DEGs # Can be informative if there are errors | |
| # There are rounding differences between different environments, e.g.: | |
| # cat analysis/DEG_lists/BaP/*_significant.txt | |
| echo "CISP DEG checksums from this run:" | |
| cat checksums.CISP_DEGs | |
| echo "CISP DEG checksums from 'truth' set:" | |
| cat truth_checksums/checksums.CISP_DEGs # Can be informative if there are errors | |
| # echo "BaP pathway checksums from this run:" | |
| # cat checksums.BaP_pathways | |
| # echo "BaP pathway checksums from 'truth' set:" | |
| # cat truth_checksums/checksums.BaP_pathways | |
| - name: Compare DEG lists to truth set | |
| run: | | |
| # Only check first column, because of timestamps in filenames | |
| # cmp <(cat truth_checksums/checksums.BaP_DEGs | awk {'print $1'} | sort) \ | |
| # <(cat checksums.BaP_DEGs | awk {'print $1'} | sort) | |
| # cmp <(cat truth_checksums/checksums.CISP_DEGs | awk {'print $1'} | sort) \ | |
| # <(cat checksums.CISP_DEGs | awk {'print $1'} | sort) | |
| # Instead of cmp, this code will check if ALL the checksums from the test have a corresponding match in the larger set of possible "truth" checksums. | |
| # This is a hack, but it should work to deal with rounding issues. | |
| diff -q <(sort -u checksums.BaP_DEGs | awk {'print $1'}) \ | |
| <(grep -Fxf \ | |
| <(cat checksums.BaP_DEGs | awk {'print $1'}) \ | |
| <(cat truth_checksums/checksums.BaP_DEGs | awk {'print $1'} | sort -u)) | |
| diff -q <(sort -u checksums.CISP_DEGs | awk {'print $1'}) \ | |
| <(grep -Fxf \ | |
| <(cat checksums.CISP_DEGs | awk {'print $1'}) \ | |
| <(cat truth_checksums/checksums.CISP_DEGs | awk {'print $1'} | sort -u)) | |
| # - name: Compare pathway analysis to truth set | |
| # run: | | |
| # cmp truth_checksums/checksums.BaP_pathways checksums.BaP_pathways | |
| - name: Compare BMD input files to truth set | |
| run: | | |
| cat checksums.BMD_files # Can be informative if there are errors | |
| cat truth_checksums/checksums.BMD_files # Can be informative if there are errors | |
| cmp <(sort -u checksums.BMD_files | awk {'print $1'}) <(sort -u truth_checksums/checksums.BMD_files | awk {'print $1'} ) |