Sync template from atomicqms-style deployment

Work-Instructions/WI-001-Template.md

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+# Work Instruction: [Title]
+
+| Document ID | WI-001 |
+|-------------|--------|
+| Title | [Title] |
+| Revision | 1.0 |
+| Effective Date | [DATE] |
+| Author | [AUTHOR] |
+| Approved By | [APPROVER] |
+| Department | Genetics & Genomics Laboratory |
+
+---
+
+## 1. Purpose
+
+[Describe the purpose of this work instruction - e.g., NGS library preparation, variant calling, DNA extraction]
+
+## 2. Scope
+
+[Define what activities this instruction covers - e.g., specific assay, platform, sample types]
+
+## 3. Safety Precautions
+
+- [List any safety requirements - biological hazards, chemical reagents]
+- [Personal protective equipment needed - lab coat, gloves, eye protection]
+- [Hazards to be aware of - ethidium bromide, formamide, liquid nitrogen]
+- [Biosafety level requirements]
+
+## 4. Equipment/Materials Required
+
+| Item | Specification | Vendor/Catalog # |
+|------|---------------|------------------|
+| [Sequencing Platform] | [Model/Version] | [Vendor] |
+| [Reagent Kit] | [Kit Name/Version] | [Catalog #] |
+| [Software] | [Version] | [Source] |
+| | | |
+
+## 5. Quality Control Materials
+
+| QC Material | Purpose | Acceptance Criteria |
+|-------------|---------|---------------------|
+| [Positive Control] | [Purpose] | [Criteria] |
+| [Negative Control] | [Purpose] | [Criteria] |
+| [Reference Standard] | [Purpose] | [Criteria] |
+
+## 6. Pre-Procedure Setup
+
+### 6.1 Sample Verification
+[Steps to verify sample identity, labeling, and chain of custody]
+
+### 6.2 Equipment Preparation
+[Equipment calibration, cleaning, initialization steps]
+
+### 6.3 Reagent Preparation
+[Reagent thawing, mixing, QC verification]
+
+## 7. Procedure
+
+### Step 1: [Title]
+[Detailed instructions with specific parameters]
+- [Sub-step with settings/values]
+- [Expected outcome/checkpoint]
+
+### Step 2: [Title]
+[Detailed instructions]
+- [Sub-step]
+- [Expected outcome/checkpoint]
+
+### Step 3: [Title]
+[Detailed instructions]
+- [Sub-step]
+- [Expected outcome/checkpoint]
+
+## 8. Quality Metrics
+
+| Metric | Target Value | Action if Out of Spec |
+|--------|--------------|----------------------|
+| [Coverage Depth] | [>20x for germline] | [Repeat sequencing] |
+| [Q30 Score] | [>80%] | [Investigate/rerun] |
+| [Uniformity] | [>0.8] | [Troubleshoot] |
+| [Contamination] | [<3%] | [Reject sample] |
+
+## 9. Acceptance Criteria
+
+[Define what constitutes successful completion]
+- [Criteria 1 with specific threshold]
+- [Criteria 2 with specific threshold]
+- [Criteria 3 with specific threshold]
+
+## 10. Troubleshooting
+
+| Problem | Possible Cause | Solution |
+|---------|----------------|----------|
+| [Issue] | [Cause] | [Action] |
+| [Issue] | [Cause] | [Action] |
+
+## 11. Records
+
+| Record | Location | Retention Period |
+|--------|----------|------------------|
+| [Run Log] | [LIMS/Path] | [CAP requirement] |
+| [QC Results] | [LIMS/Path] | [Minimum 2 years] |
+| [Variant Call Files] | [Secure Storage] | [Per CLIA/CAP] |
+
+## 12. Data Management
+
+- [File naming conventions]
+- [Data backup procedures]
+- [Version control for pipelines/software]
+- [Data retention and archival]
+
+## 13. References
+
+### Related SOPs
+- [SOP-SEQ-XXX: NGS Quality Control]
+- [SOP-DM-XXX: Bioinformatics Data Management]
+- [SOP-GEN-XXX: Sample Tracking]
+
+### Manufacturer Documentation
+- [Instrument User Guide, Version X]
+- [Reagent Kit Insert, Version X]
+- [Software Manual, Version X]
+
+### Standards and Guidelines
+- [CAP Molecular Pathology Checklist]
+- [CLIA requirements]
+- [Relevant professional guidelines]
+
+---
+
+## Revision History
+
+| Rev | Date | Description | Author |
+|-----|------|-------------|--------|
+| 1.0 | [DATE] | Initial release | [AUTHOR] |