check-release.yaml

# 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)