(input_mode: str)
| 131 | |
| 132 | |
| 133 | def build_outputs_map(input_mode: str) -> dict[str, str]: |
| 134 | outputs = { |
| 135 | "contrast_status": "manifest/contrast_status.tsv", |
| 136 | "qc_plots": "qc/*.png", |
| 137 | "de_tables": "results/*.tsv", |
| 138 | "contrast_plots": "plots/*.png", |
| 139 | "design_diagnostics": "qc/design_diagnostics.tsv", |
| 140 | "outlier_metrics": "qc/sample_outlier_metrics.tsv", |
| 141 | "statistical_summary": "qc/statistical_summary.tsv", |
| 142 | "statistical_warnings": "qc/statistical_warnings.tsv", |
| 143 | } |
| 144 | if input_mode == "raw_counts": |
| 145 | outputs.update( |
| 146 | { |
| 147 | "raw_counts": "results/raw_counts.tsv", |
| 148 | "normalized_expression": "results/normalized_expression_matrix.tsv", |
| 149 | "log_expression": "results/log2_expression_matrix.tsv", |
| 150 | } |
| 151 | ) |
| 152 | elif input_mode == "normalized_expression": |
| 153 | outputs.update( |
| 154 | { |
| 155 | "input_normalized_expression": "results/input_normalized_expression_matrix.tsv", |
| 156 | "log_expression": "results/log2_expression_matrix.tsv", |
| 157 | } |
| 158 | ) |
| 159 | else: |
| 160 | outputs.update( |
| 161 | { |
| 162 | "input_log_expression": "results/input_log_expression_matrix.tsv", |
| 163 | "modeling_expression": "results/modeling_expression_matrix.tsv", |
| 164 | } |
| 165 | ) |
| 166 | return outputs |
| 167 | |
| 168 | |
| 169 | def validate_inputs(args: argparse.Namespace) -> tuple[dict[str, Any], dict[str, Any]]: |
no outgoing calls
no test coverage detected