Fix assay logging in app building #147
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| pull_request: | |
| branches: [develop] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.R_CI }} | |
| R_KEEP_PKG_SOURCE: yes | |
| TEST_DATA_BASE: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/mus_musculus/rnaseq_expression" | |
| FEATURE_META_FILE: "SRP254919.gene_meta.tsv" | |
| SAMPLE_META_FILE: "SRP254919.samplesheet.csv" | |
| ASSAY_FILE: "SRP254919.salmon.merged.gene_counts.top1000cov.tsv" | |
| CONTRASTS_FILE: "SRP254919.contrasts.csv" | |
| DIFFERENTIAL_FILE: "SRP254919.salmon.merged.deseq2.results.tsv" | |
| TREATMENT_VARIABLE: "treatment" | |
| REFERENCE_LEVEL: "mCherry" | |
| TREATMENT_LEVEL: "hND6" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck, local::. | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| error-on: '"error"' | |
| args: 'c("--no-manual", "--as-cran", "--no-examples")' | |
| - name: Download test data from nf-core tests data repo | |
| run: | | |
| for filename in $CONTRASTS_FILE $FEATURE_META_FILE $SAMPLE_META_FILE $ASSAY_FILE $DIFFERENTIAL_FILE; do | |
| wget -O $filename ${TEST_DATA_BASE}/$filename | |
| done | |
| - name: Run FOM validation script | |
| run: | | |
| ./exec/validate_fom_components.R \ | |
| --sample_metadata $SAMPLE_META_FILE \ | |
| --feature_metadata $FEATURE_META_FILE \ | |
| --assay_files $ASSAY_FILE \ | |
| --contrasts_file $CONTRASTS_FILE \ | |
| --output_directory $(pwd) | |
| - name: Run exploratory plots script | |
| run: | | |
| ./exec/exploratory_plots.R \ | |
| --sample_metadata $SAMPLE_META_FILE \ | |
| --feature_metadata $FEATURE_META_FILE \ | |
| --assay_files $ASSAY_FILE \ | |
| --contrast_variable $TREATMENT_VARIABLE \ | |
| --outdir $(pwd) | |
| - name: Run differential plots script | |
| run: | | |
| ./exec/differential_plots.R \ | |
| --differential_file $DIFFERENTIAL_FILE \ | |
| --feature_metadata $FEATURE_META_FILE \ | |
| --reference_level $REFERENCE_LEVEL \ | |
| --treatment_level $TREATMENT_LEVEL \ | |
| --outdir $(pwd) | |
| - name: Run app-building script | |
| run: | | |
| ln -s $DIFFERENTIAL_FILE copied_${DIFFERENTIAL_FILE} | |
| ./exec/make_app_from_files.R \ | |
| --sample_metadata $SAMPLE_META_FILE \ | |
| --feature_metadata $FEATURE_META_FILE \ | |
| --assay_files $ASSAY_FILE \ | |
| --contrast_file $CONTRASTS_FILE \ | |
| --contrast_stats_assay 1 \ | |
| --differential_results ${DIFFERENTIAL_FILE},copied_${DIFFERENTIAL_FILE} \ | |
| --output_dir $(pwd) | |