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Pull request overview
This PR renames the GENOS wide-table score column and related pipeline/reporting references from GENOS-EVEE to GENOS-VarRisk, updating both the pipeline output and the pixi report ingestion/docs accordingly.
Changes:
- Rename wide-table column header and downstream parsing from
GENOS-EVEE→GENOS-VarRisk. - Update pipeline CLI/API flags, help text, and module documentation to reference
GENOS-VarRisk. - Refresh demo fixtures/examples to use the new column name.
Reviewed changes
Copilot reviewed 18 out of 18 changed files in this pull request and generated 14 comments.
Show a summary per file
| File | Description |
|---|---|
| modules/pixi_report/scripts/export_report.py | Updates PDF preprocessing header detection for the renamed label. |
| modules/pixi_report/report/wide_table.py | Switches wide-table ingestion to read GENOS-VarRisk. |
| modules/pixi_report/README.md | Documents the wide-table column rename for pixi_report inputs. |
| modules/pixi_report/examples/demo_case/wide_table.csv | Updates demo wide-table header to GENOS-VarRisk. |
| modules/pixi_report/examples/demo_case/output/report.md | Updates demo report output labels to the new name. |
| modules/pipeline/test/run_mock_smoke_dryrun.sh | Updates mock smoke test invocation flag for the renamed DB option. |
| modules/pipeline/scripts/run_full_pipeline.sh | Renames CLI flag and updates help/error text to GENOS-VarRisk. |
| modules/pipeline/resource_mock/README.md | Updates dry-run example to use the renamed CLI flag. |
| modules/pipeline/README.md | Updates pipeline overview and output header examples to GENOS-VarRisk. |
| modules/pipeline/modules/vcf_info_to_csv/README.md | Updates step description to reference GENOS-VarRisk. |
| modules/pipeline/modules/result_sorting/README.md | Updates module docs to reference GENOS-VarRisk column. |
| modules/pipeline/modules/hla_filter/README.md | Updates module docs to reference GENOS-VarRisk. |
| modules/pipeline/modules/genos_evee_annotation/scripts/build_genos_evee_db.py | Updates database header and CLI description string to GENOS-VarRisk. |
| modules/pipeline/modules/genos_evee_annotation/scripts/add_genos_evee_to_csv.py | Changes output column name and related messages to GENOS-VarRisk. |
| modules/pipeline/modules/genos_evee_annotation/README.md | Updates module naming/docs and CLI example to GENOS-VarRisk. |
| modules/pipeline/EXTERNAL_PATHS.md | Updates external paths doc to label step 06 output as GENOS-VarRisk. |
| modules/pipeline/complete_pipeline/README.md | Updates API-to-CLI flag mapping and narrative to GENOS-VarRisk. |
| modules/pipeline/complete_pipeline/full_pipeline_api.py | Updates FastAPI runner to emit the renamed CLI flag and description. |
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Owner
|
OK |
| ppi_final=_display(row.get("ppi_final")), | ||
| evidence_summary=_display(row.get("evidence_summary")), | ||
| genos_evee=_display(row.get("GENOS-EVEE")), | ||
| genos_evee=_display(row.get("GENOS-VarRisk")), |
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| | GENOS-VarRisk | - | | ||
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| #### 3.1.2 变异列表 | ||
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| | 变异 | 转录本 / 后果 | GENOS-EVEE | 评分 | ClinVar（VAF） | | ||
| | 变异 | 转录本 / 后果 | GENOS-VarRisk | 评分 | ClinVar（VAF） | |
| | 转录本 | ENST00000692443.1 | | ||
| | RefSeq | NM_033554.4,NM_001405020.1 | | ||
| | GENOS-EVEE | - | | ||
| | GENOS-VarRisk | - | |
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| | GENOS-VarRisk | - | | ||
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| #### 3.2.2 变异列表 | ||
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| | 变异 | 转录本 / 后果 | GENOS-EVEE | 评分 | ClinVar（VAF） | | ||
| | 变异 | 转录本 / 后果 | GENOS-VarRisk | 评分 | ClinVar（VAF） | |
| | 转录本 | ENST00000601181.6 | | ||
| | RefSeq | NM_198477.3 | | ||
| | GENOS-EVEE | - | | ||
| | GENOS-VarRisk | - | |
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| | GENOS-VarRisk | - | | ||
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| #### 3.3.2 变异列表 | ||
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| | 变异 | 转录本 / 后果 | GENOS-EVEE | 评分 | ClinVar（VAF） | | ||
| | 变异 | 转录本 / 后果 | GENOS-VarRisk | 评分 | ClinVar（VAF） | |
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| | GENOS-VarRisk | - | | ||
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| #### 3.4.2 变异列表 | ||
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| | 变异 | 转录本 / 后果 | GENOS-EVEE | 评分 | ClinVar（VAF） | | ||
| | 变异 | 转录本 / 后果 | GENOS-VarRisk | 评分 | ClinVar（VAF） | |
xhli2
requested changes
Jun 29, 2026
xhli2
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xhli2
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Collaborator
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在report 部分展示的还是genos-mutation ,之前的流程是从宽表读取genos-evee ，然后展示为genos-mutation ,现在只改了genos-evee
Collaborator
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ok |
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