i pointed it at an existing s3 location that doesnt' actually contain the igenome ref but is readable by the pipeline and it is proceeding - probably a bug worth looking at - should I report on the github issue tracker?

Hi @Marshall Thompson, would you be able to post here the error message and a general description of your setup?

Hi @Stephen Watts The setup is running oncoanalyser in AWS HealthOmics All of the documented required reference data is staged in S3 For parameters, I specifically set ignore_igenomes to "true" When the pipeline starts, it fails with

ERROR n.m.d.s3.v2.S3FileSystemProviderV2 - Failed to read S3 object attributes for /ngi-igenomes/igenomes/
software.amazon.awssdk.core.exception.SdkClientException: Unable to execute HTTP request: Connect to <http://ngi-igenomes.s3.eu-west-1.amazonaws.com:443|ngi-igenomes.s3.eu-west-1.amazonaws.com:443> [<http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.64.3|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.64.3>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.66.3|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.66.3>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/52.92.32.138|ngi-igenomes.s3.eu-west-1.amazonaws.com/52.92.32.138>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.70.192|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.70.192>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.71.85|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.71.85>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.71.114|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.71.114>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.67.201|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.67.201>, <http://ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.69.9]|ngi-igenomes.s3.eu-west-1.amazonaws.com/3.5.69.9]> failed: Connect timed out (SDK Attempt Count: 4)

Presumably something in the nf-core plumbing is still checking access to the default igenomes path even though the ignore flag is set Setting the igenomes_base URL to something in S3 that my instance can read (but doesnt actually have the full igenomes reference) succeeds

Thanks for the feedback, I’ll set aside some time next week to look at this more closely