(args: argparse.Namespace)
| 111 | |
| 112 | |
| 113 | def validate_inputs(args: argparse.Namespace) -> tuple[dict[str, Any], list[dict[str, str]]]: |
| 114 | sample_sheet = args.sample_sheet.expanduser().resolve() |
| 115 | errors: list[str] = [] |
| 116 | warnings: list[str] = [] |
| 117 | pairs: list[dict[str, str]] = [] |
| 118 | rows: list[dict[str, str]] = [] |
| 119 | columns: list[str] = [] |
| 120 | if not sample_sheet.exists(): |
| 121 | errors.append(f"sample sheet does not exist: {sample_sheet}") |
| 122 | else: |
| 123 | try: |
| 124 | rows, columns = read_table(sample_sheet) |
| 125 | except Exception as exc: # pragma: no cover - defensive parser guard |
| 126 | errors.append(f"failed to parse sample sheet {sample_sheet}: {exc}") |
| 127 | |
| 128 | reference = optional_existing_path( |
| 129 | str(args.reference_fasta), |
| 130 | sample_sheet.parent, |
| 131 | errors, |
| 132 | warnings, |
| 133 | "reference FASTA", |
| 134 | required=True, |
| 135 | ) |
| 136 | if reference: |
| 137 | if not Path(str(reference) + ".fai").exists(): |
| 138 | warnings.append( |
| 139 | f"reference FASTA index is missing and may be created by samtools faidx: {reference}.fai" |
| 140 | ) |
| 141 | if not reference.with_suffix(".dict").exists(): |
| 142 | warnings.append( |
| 143 | f"reference sequence dictionary is missing and may be created by GATK: {reference.with_suffix('.dict')}" |
| 144 | ) |
| 145 | target_bed = optional_existing_path( |
| 146 | str(args.target_bed) if args.target_bed else None, |
| 147 | sample_sheet.parent, |
| 148 | errors, |
| 149 | warnings, |
| 150 | "target BED", |
| 151 | ) |
| 152 | panel_of_normals = optional_existing_path( |
| 153 | str(args.panel_of_normals) if args.panel_of_normals else None, |
| 154 | sample_sheet.parent, |
| 155 | errors, |
| 156 | warnings, |
| 157 | "panel-of-normals VCF", |
| 158 | ) |
| 159 | germline_resource = optional_existing_path( |
| 160 | str(args.germline_resource) if args.germline_resource else None, |
| 161 | sample_sheet.parent, |
| 162 | errors, |
| 163 | warnings, |
| 164 | "germline resource VCF", |
| 165 | ) |
| 166 | annotation_vcf = optional_existing_path( |
| 167 | str(args.annotation_vcf) if args.annotation_vcf else None, |
| 168 | sample_sheet.parent, |
| 169 | errors, |
| 170 | warnings, |
no test coverage detected