Command Line Interface (CLI)
kreview exposes all primary pipeline orchestrations explicitly through the terminal using typer.
kreview
ctDNA fragmentomics feature evaluation
Usage:
Options:
--version
--install-completion Install completion for the current shell.
--show-completion Show completion for the current shell, to copy it or
customize the installation.
features-list
List all registered feature evaluators.
Usage:
label
Generate ctDNA labels without feature evaluation.
Usage:
Options:
--cancer-samplesheet PATH Cancer samplesheet CSV [required]
--healthy-xs1-samplesheet PATH Healthy XS1 samplesheet CSV [required]
--healthy-xs2-samplesheet PATH Healthy XS2 samplesheet CSV [required]
--cbioportal-dir PATH Directory with cBioPortal files [required]
--output PATH Output parquet file [default:
labels.parquet]
--min-vaf FLOAT Min VAF for Possible ctDNA+ (default 1%)
[default: 0.01]
--min-variants INTEGER Min # variants passing VAF for Possible
ctDNA+ [default: 1]
--chunk-size INTEGER Batch size for DuckDB file loading over SFTP
network mounts [default: 500]
report
Re-generate HTML Dashboards from existing matrix parquet files.
Usage:
Options:
--input-dir PATH Directory with *_matrix.parquet files [required]
--out-dir PATH Directory to deposit Quarto reports [default:
reports/]
--cvd-safe Render dashboards and plots using an Okabe-Ito
Colorblind-Safe palette instead of default neon.
--shap-samples INTEGER Max samples for SHAP explainability computation in
dashboards. [default: 500]
--shap-features INTEGER Max features to visualize in SHAP plots. [default:
10]
run
Run full pipeline: label → extract → evaluate → report.
Usage:
Options:
--cancer-samplesheet PATH [required]
--healthy-xs1-samplesheet PATH [required]
--healthy-xs2-samplesheet PATH [required]
--cbioportal-dir PATH [required]
--krewlyzer-dir TEXT krewlyzer output directory [required]
--output PATH Output directory [default: output/]
--min-vaf FLOAT [default: 0.01]
--min-fragments INTEGER [default: 2000]
--min-variants INTEGER [default: 1]
--features TEXT Comma-separated features to run
--tier INTEGER Run features of this tier only
--workers INTEGER Total processes [default: 4]
-v, --verbose Enable verbose logging
--cvd-safe Render dashboards and plots using an Okabe-
Ito Colorblind-Safe palette instead of
default neon.
--skip-report / --no-skip-report
Skip HTML report generation [default: no-
skip-report]
--cv-folds INTEGER Number of cross-validation folds (3-20,
default 5) [default: 5]
--impute-strategy TEXT Imputation strategy for missing values:
median, mean, or zero [default: median]
--export-duckdb Export a persistent duckdb data lake
containing all feature matrices
--chunk-size INTEGER Batch size for DuckDB file loading over SFTP
network mounts [default: 500]
--top-n INTEGER Max sub-metrics to feed into ML models per
evaluator. All sub-metrics are included up
to this cap; the model's feature importance
ranks them. [default: 50]
--shap-samples INTEGER Max samples for SHAP explainability
computation in dashboards. Lower values
reduce memory usage. [default: 500]
--shap-features INTEGER Max features to visualize in SHAP
beeswarm/waterfall plots. The model still
trains on --top-n features. [default: 10]
--resume Skip evaluators whose model results already
exist in the output directory.
--compute-univariate-auc Compute per-feature univariate LR AUC (adds
~10s per evaluator).