(args: argparse.Namespace)
| 35 | |
| 36 | |
| 37 | def validate_inputs(args: argparse.Namespace) -> tuple[dict[str, Any], list[dict[str, str]]]: |
| 38 | sample_sheet = args.sample_sheet.expanduser().resolve() |
| 39 | errors: list[str] = [] |
| 40 | warnings: list[str] = [] |
| 41 | rows: list[dict[str, str]] = [] |
| 42 | columns: list[str] = [] |
| 43 | samples: list[dict[str, str]] = [] |
| 44 | if not sample_sheet.exists(): |
| 45 | errors.append(f"sample sheet does not exist: {sample_sheet}") |
| 46 | else: |
| 47 | rows, columns = read_table(sample_sheet) |
| 48 | if not args.bam_only and not args.bowtie2_index: |
| 49 | warnings.append( |
| 50 | "no --bowtie2-index was provided; FASTQ rows can only be planned, not aligned" |
| 51 | ) |
| 52 | if not args.genome_size: |
| 53 | errors.append( |
| 54 | "--genome-size is required for MACS2 peak calling, e.g. hs, mm, or an effective genome size" |
| 55 | ) |
| 56 | blacklist = args.blacklist_bed.expanduser().resolve() if args.blacklist_bed else None |
| 57 | if blacklist and not blacklist.exists(): |
| 58 | errors.append(f"blacklist BED does not exist: {blacklist}") |
| 59 | tss_bed = args.tss_bed.expanduser().resolve() if args.tss_bed else None |
| 60 | if tss_bed and not tss_bed.exists(): |
| 61 | warnings.append( |
| 62 | f"TSS BED does not exist; TSS enrichment commands will be skipped: {tss_bed}" |
| 63 | ) |
| 64 | if getattr(args, "run_motifs", False) and not getattr(args, "motif_genome", None): |
| 65 | errors.append( |
| 66 | "--run-motifs requires --motif-genome, for example hg38, mm10, or a HOMER genome identifier" |
| 67 | ) |
| 68 | |
| 69 | for row_index, row in enumerate(rows, start=2): |
| 70 | sample = normalize_sample_name( |
| 71 | row.get("sample") or row.get("sample_id"), f"row_{row_index}" |
| 72 | ) |
| 73 | bam = resolve_path(row.get("bam") or row.get("alignment"), sample_sheet.parent) |
| 74 | r1 = resolve_path(row.get("r1") or row.get("fastq_1"), sample_sheet.parent) |
| 75 | r2 = resolve_path(row.get("r2") or row.get("fastq_2"), sample_sheet.parent) |
| 76 | if bam: |
| 77 | if not bam.exists(): |
| 78 | errors.append(f"row {row_index}: BAM does not exist: {bam}") |
| 79 | layout = "bam" |
| 80 | elif r1: |
| 81 | if not r1.exists(): |
| 82 | errors.append(f"row {row_index}: R1 FASTQ does not exist: {r1}") |
| 83 | if r2 and not r2.exists(): |
| 84 | errors.append(f"row {row_index}: R2 FASTQ does not exist: {r2}") |
| 85 | layout = "fastq_pe" if r2 else "fastq_se" |
| 86 | else: |
| 87 | errors.append(f"row {row_index}: provide bam/alignment or r1/fastq_1") |
| 88 | continue |
| 89 | samples.append( |
| 90 | { |
| 91 | "sample": sample, |
| 92 | "condition": row.get("condition", ""), |
| 93 | "replicate": row.get("replicate", ""), |
| 94 | "layout": layout, |
no test coverage detected