From 9dcf05c0c05ff6d240128b896c8ca42a18e579e7 Mon Sep 17 00:00:00 2001 From: Tejas Dharani Date: Tue, 7 Apr 2026 14:13:03 +0530 Subject: [PATCH] fix(bio-research): download FASTQ files over HTTPS instead of HTTP ENA FTP paths were converted to plain HTTP URLs, meaning multi-GB genomic downloads had no transport-layer encryption. ENA supports HTTPS on the same paths. Changed http:// to https:// on line 343. Fixes #166 --- .../skills/nextflow-development/scripts/utils/ncbi_utils.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bio-research/skills/nextflow-development/scripts/utils/ncbi_utils.py b/bio-research/skills/nextflow-development/scripts/utils/ncbi_utils.py index a331d613..44743a03 100644 --- a/bio-research/skills/nextflow-development/scripts/utils/ncbi_utils.py +++ b/bio-research/skills/nextflow-development/scripts/utils/ncbi_utils.py @@ -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