My Nextflow pipeline downloads a reference genome by passing the URL as a process input path. This has worked consistently until today, when I started getting the error:
Can't stage file https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz -- reason: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
On the same computer where I’m getting this error, I can manually download the file using this URL in my browser. I also can download it by using curl in the staging process command. This isn’t a great solution however, because the user can also pass a local reference rather than a URL, and I had wanted Nextflow to manage staging files when necessary. Any idea what might be causing this error?