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fix(bio-research): download FASTQ files over HTTPS instead of HTTP #173

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fix(bio-research): download FASTQ files over HTTPS instead of HTTP #173

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6 changes: 3 additions & 3 deletions bio-research/skills/nextflow-development/scripts/utils/ncbi_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -338,9 +338,9 @@ def fetch_ena_fastq_urls(study_accession: str) -> Dict[str, List[str]]:
srr = fields[run_idx]
ftp_urls = fields[ftp_idx]
if ftp_urls:
# URLs are semicolon-separated, convert to HTTP URLs
# ENA supports both FTP and HTTP, HTTP is easier with requests
urls = [f"http://{url}" for url in ftp_urls.split(';') if url]
# URLs are semicolon-separated, convert to HTTPS URLs
# ENA supports HTTPS for encrypted downloads
urls = [f"https://{url}" for url in ftp_urls.split(';') if url]
fastq_urls[srr] = urls

return fastq_urls
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