Fix assay logging in app building #148
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
| # 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) | |