/wes-clinical-report-es

name: wes-clinical-report-es
description: Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation,
  pharmacogenomic alerts, and follow-up recommendations.
license: PROPRIETARY
metadata:
  version: 1.0.0
  author: Manuel Corpas
  tags:
  - WES
  - exome
  - clinical-report
  - spanish
  - pharmacogenomics
  - PDF
  - ANNOVAR
  inputs:
  - name: WES markdown report
    format: markdown (.md)
    required: true
    description: Structured WES report with sections 1-7 (Exome Summary through Methods)
  - name: Logo left (Predice)
    format: image (JPG/PNG)
    required: false
    description: Predice institutional logo for cover and header
  - name: Logo right (Inbiomedic)
    format: image (JPG/PNG)
    required: false
    description: Inbiomedic institutional logo for cover and header
  outputs:
  - name: Clinical PDF report (Spanish)
    format: PDF (A4)
    description: Professional clinical report in Spanish with interpretation, tables, and disclaimer
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 🧬
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    min_python: '3.9'
    dependencies:
    - reportlab
    - pandas
    private: true
    trigger_keywords:
    - informe clinico WES
    - clinical report spanish
    - exome PDF report
    - Novogene report
    - Predice
    - Inbiomedic

Informe Clinico WES en Espanol

Skill for generating professional clinical PDF reports in Spanish from whole exome sequencing (WES) data. Designed for Novogene WES data (GATK + ANNOVAR pipeline) but adaptable to any WES pipeline with equivalent annotations. Translates all section headings, table headers, cell values, and interpretive text from English markdown input to Spanish PDF output.

Trigger

**Fire this skill when the user says any of:**

• "informe clinico WES"
• "generar informe exoma en espanol"
• "clinical report in Spanish"
• "Novogene report Spanish"
• "exome PDF report Spanish"
• "Predice/Inbiomedic report"

**Do NOT fire when:**

• User asks for an English report (use `wes-clinical-report-en`)
• User asks for variant annotation only (use `variant-annotation`)
• User asks for ACMG classification only (use `clinical-variant-reporter`)

Scope

One skill, one task: convert WES markdown reports (English input) into professional Spanish-language clinical PDFs with full translation and clinical interpretation.

Workflow

1. Parse WES markdown report (structured sections 1-7) 2. Extract KPI metrics from Exome Summary 3. Extract pathogenic variants, PGx alerts, rare damaging variants 4. Translate all headings, table headers, cell values, and body text to Spanish 5. Build interpretive summary paragraph in Spanish 6. Render all sections as styled PDF with clinical tables 7. Add ancestry estimation (section 8) if data available 8. Add limitations section (section 9) in Spanish 9. Add Spanish disclaimer and report metadata 10. Output PDF to specified directory

Capabilities

1. **Clinical interpretation summary (Spanish)**: key findings, high-risk PGx alerts, prioritised rare variants, clinical follow-up recommendations. 2. **Full translation layer**: section headings, table headers, metric labels, zygosity, classification, consequence, clinical effects, traits, and interpretations all translated via lookup dictionaries. 3. **Clinically significant variants**: ClinVar P/LP, ACMG SF v3.2, cancer predisposition panel, conflicting variants. 4. **Pharmacogenomics**: CPIC star alleles, clinical effects, affected medications with contextualised high-risk alerts. 5. **Fitness and nutrition traits**: genotypes with evidence grades (Corpas et al. 2021). 6. **Rare damaging variant prioritisation**: REVEL, CADD, gnomAD AF. 7. **Institutional logos**: Predice (left) and Inbiomedic (right) on cover and header.

Example Output

Pagina 1 (portada):
  [Logo Predice]                    [Logo Inbiomedic]
  +---------------------------------------------+
  |  Secuenciacion del Exoma Completo  [SampleN]|
  |  Plataforma / Referencia / Fecha            |
  +---------------------------------------------+
  [KPIs: SNPs Totales | Missense | Stopgain | Raras Patog. | ClinVar P/PP]

  Interpretacion de resultados
  (parrafo interpretativo clinico auto-generado en espanol)

Paginas 2+:
  1. Resumen del Exoma
  2. Variantes de Significancia Clinica
  3. Farmacogenomica
  4. Rasgos de Aptitud Fisica y Nutricion
  5. Variantes Raras Patogenicas Priorizadas
  6. Contexto de Enfermedad y Vias Metabolicas
  7. Metodologia
  8. Estimacion de Ancestria
  9. Limitaciones
  [Aviso legal / Disclaimer]

Usage

# Generate reports for all samples
python skills/wes-clinical-report-es/wes_clinical_report_es.py \
  --report-dir /path/to/REPORTS/ \
  --output-dir /path/to/PDF-ES/ \
  --logo-left /path/to/logo_predice.jpg \
  --logo-right /path/to/logo_inbiomedic.jpg

# Generate report for a single sample
python skills/wes-clinical-report-es/wes_clinical_report_es.py \
  --report-dir /path/to/REPORTS/ \
  --output-dir /path/to/PDF-ES/ \
  --samples Sample3

# Demo with default Novogene data
python skills/wes-clinical-report-es/wes_clinical_report_es.py --demo

Input format

The skill consumes WES reports in markdown format generated by the analysis pipeline (scripts 02-12 in `ANALYSIS/SCRIPTS/`). Each markdown report must follow this structure:

# Whole Exome Sequencing Report: SampleN
> **Project** ... | **Platform** ... | ...
## 1. Exome Summary
## 2. Clinically Significant Variants
## 3. Pharmacogenomics
## 4. Fitness and Nutrition Traits
## 5. Prioritised Rare Damaging Variants
## 6. Disease and Pathway Context
## 7. Methods

Gotchas

1. **Input is English, output is Spanish**: the markdown reports are in English. The skill translates to Spanish via dictionary lookups. If a term is missing from the translation dictio