chore: import upstream snapshot with attribution

bio-research/skills/nextflow-development/scripts/utils/__init__.py

@@ -0,0 +1,69 @@
+"""
+Utility modules for nf-core pipeline deployment.
+
+Modules:
+    ncbi_utils: NCBI/GEO/SRA data fetching and download utilities
+    file_discovery: Find FASTQ, BAM, and CRAM files
+    sample_inference: Extract sample info, detect tumor/normal
+    validators: Validate samplesheets before writing
+"""
+
+# NCBI utilities for GEO/SRA data acquisition
+from .ncbi_utils import (
+    check_network_access,
+    fetch_geo_metadata,
+    fetch_sra_study_accession,
+    fetch_sra_run_info,
+    fetch_sra_run_info_detailed,
+    fetch_bioproject_from_geo,
+    fetch_ena_fastq_urls,
+    download_file,
+    fetch_pubmed_metadata,
+    format_file_size,
+    estimate_download_size,
+    group_samples_by_type,
+    format_sample_groups_table,
+)
+
+# File discovery utilities
+from .file_discovery import discover_files, FileInfo, count_files_by_type
+
+# Sample inference utilities
+from .sample_inference import (
+    extract_sample_info,
+    infer_tumor_normal_status,
+    match_read_pairs,
+    extract_replicate_number
+)
+
+# Validation utilities
+from .validators import validate_samplesheet, ValidationResult
+
+__all__ = [
+    # ncbi_utils
+    'check_network_access',
+    'fetch_geo_metadata',
+    'fetch_sra_study_accession',
+    'fetch_sra_run_info',
+    'fetch_sra_run_info_detailed',
+    'fetch_bioproject_from_geo',
+    'fetch_ena_fastq_urls',
+    'download_file',
+    'fetch_pubmed_metadata',
+    'format_file_size',
+    'estimate_download_size',
+    'group_samples_by_type',
+    'format_sample_groups_table',
+    # file_discovery
+    'discover_files',
+    'FileInfo',
+    'count_files_by_type',
+    # sample_inference
+    'extract_sample_info',
+    'infer_tumor_normal_status',
+    'match_read_pairs',
+    'extract_replicate_number',
+    # validators
+    'validate_samplesheet',
+    'ValidationResult',
+]