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The error says that access was denied to a file under

<s3://alices-r2-bucket/test_full/out/>

, which I assume is your

--output

directory, so this does not seem related to the AWS S3 bucket ... Are you supplying the correct Cloudflare R2 credentials? I have no experience with using Nextflow in the cloud, but I remember people having issues accessing e.g. the iGenomes S3 bucket while using their own AWS S3 bucket(s), since the credential were applied to both (not sure if that has been fixed since). That seems to be a different issue from yours, though.