Tighten PharmCAT and PRS maintenance guidance #23
Workflow file for this run
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| name: Smoke Tests | |
| on: | |
| push: | |
| branches: [main] | |
| paths: ['scripts/**', '.github/workflows/smoke-test.yml'] | |
| pull_request: | |
| branches: [main] | |
| paths: ['scripts/**', '.github/workflows/smoke-test.yml'] | |
| jobs: | |
| contract-validation: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Verify ClinVar artifact contract is consistent | |
| run: | | |
| echo "Checking ClinVar path contract across scripts..." | |
| FAIL=0 | |
| # setup.sh must create clinvar_chr.vcf.gz (chr-renamed) before clinvar_pathogenic_chr.vcf.gz | |
| if ! grep -q 'clinvar_chr.vcf.gz' scripts/setup.sh; then | |
| echo "FAIL: setup.sh does not create clinvar_chr.vcf.gz (chr-renamed ClinVar)" | |
| FAIL=1 | |
| fi | |
| # setup.sh must filter from clinvar_chr (not raw clinvar.vcf.gz) | |
| if grep 'clinvar.vcf.gz -Oz' scripts/setup.sh | grep -qv 'clinvar_chr'; then | |
| echo "FAIL: setup.sh filters from raw ClinVar instead of chr-renamed" | |
| FAIL=1 | |
| fi | |
| # setup.sh must include Likely_pathogenic | |
| if ! grep -q 'Likely_pathogenic' scripts/setup.sh; then | |
| echo "FAIL: setup.sh does not include Likely_pathogenic variants" | |
| FAIL=1 | |
| fi | |
| # validate-setup.sh must check clinvar_pathogenic_chr.vcf.gz (what step 6 uses) | |
| if ! grep -q 'clinvar_pathogenic_chr\|clinvar_chr' scripts/validate-setup.sh; then | |
| echo "FAIL: validate-setup.sh does not check the ClinVar file step 6 needs" | |
| FAIL=1 | |
| fi | |
| # step 6 must use clinvar/clinvar_pathogenic_chr.vcf.gz | |
| if ! grep -q 'clinvar/clinvar_pathogenic_chr.vcf.gz' scripts/06-clinvar-screen.sh; then | |
| echo "FAIL: step 6 does not reference clinvar/clinvar_pathogenic_chr.vcf.gz" | |
| FAIL=1 | |
| fi | |
| [ "$FAIL" -eq 0 ] && echo "OK: ClinVar contract is consistent" | |
| exit "$FAIL" | |
| - name: Verify output paths in HTML report match actual scripts | |
| run: | | |
| echo "Checking HTML report path references..." | |
| FAIL=0 | |
| # Haplogroup must reference mito/ (not haplogrep/) — exclude comments | |
| if grep -v '^\s*#' scripts/24-html-report.sh | grep -q 'haplogrep/'; then | |
| echo "FAIL: HTML report references haplogrep/ but step 12 writes to mito/" | |
| FAIL=1 | |
| fi | |
| # Mitochondrial must reference mito/ (not mtoolbox/) — exclude comments | |
| if grep -v '^\s*#' scripts/24-html-report.sh | grep -q 'mtoolbox/'; then | |
| echo "FAIL: HTML report references mtoolbox/ but step 20 writes to mito/" | |
| FAIL=1 | |
| fi | |
| # Clinical filter must reference clinical/ (not vep/) — exclude comments | |
| if grep -v '^\s*#' scripts/24-html-report.sh | grep 'clinical.*vcf.gz' | grep -q '/vep/'; then | |
| echo "FAIL: HTML report looks for clinical VCF in vep/ instead of clinical/" | |
| FAIL=1 | |
| fi | |
| [ "$FAIL" -eq 0 ] && echo "OK: HTML report paths are consistent" | |
| exit "$FAIL" | |
| - name: Verify Docker image tags are consistent | |
| run: | | |
| echo "Checking Docker image consistency between setup.sh and scripts..." | |
| FAIL=0 | |
| # Extract images from setup.sh | |
| SETUP_IMAGES=$(grep -oP '"[^"]+:[^"]+"' scripts/setup.sh | tr -d '"' | sort) | |
| # Check key images used in scripts are also in setup.sh | |
| for IMG in "python:3.11-slim" "pgscatalog/plink2:2.00a5.10"; do | |
| if ! echo "$SETUP_IMAGES" | grep -qF "$IMG"; then | |
| echo "FAIL: $IMG used in scripts but not in setup.sh image list" | |
| FAIL=1 | |
| fi | |
| done | |
| # Check t1k tag matches | |
| SETUP_T1K=$(echo "$SETUP_IMAGES" | grep t1k || true) | |
| SCRIPT_T1K=$(grep -roh 't1k:[^ "]*' scripts/08-hla-typing.sh 2>/dev/null | head -1 || true) | |
| if [ -n "$SETUP_T1K" ] && [ -n "$SCRIPT_T1K" ] && [ "$SETUP_T1K" != "$SCRIPT_T1K" ]; then | |
| echo "WARN: t1k tag mismatch: setup=$SETUP_T1K script=$SCRIPT_T1K" | |
| fi | |
| [ "$FAIL" -eq 0 ] && echo "OK: Docker images are consistent" | |
| exit "$FAIL" | |
| - name: Verify experimental steps are marked | |
| run: | | |
| echo "Checking experimental step markers..." | |
| FAIL=0 | |
| for SCRIPT in scripts/21-cyrius.sh scripts/22-survivor-merge.sh scripts/26-ancestry.sh; do | |
| if [ -f "$SCRIPT" ] && ! head -5 "$SCRIPT" | grep -qi 'experimental'; then | |
| echo "FAIL: $SCRIPT should be marked as EXPERIMENTAL" | |
| FAIL=1 | |
| fi | |
| done | |
| [ "$FAIL" -eq 0 ] && echo "OK: Experimental steps are properly marked" | |
| exit "$FAIL" | |
| shellcheck-new-steps: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: ShellCheck steps 21-27 | |
| uses: ludeeus/action-shellcheck@master | |
| with: | |
| scandir: scripts | |
| additional_files: '21-cyrius.sh 22-survivor-merge.sh 23-clinical-filter.sh 24-html-report.sh 25-prs.sh 26-ancestry.sh 27-cpic-lookup.sh' | |
| severity: warning |