Brad Chapman

Thanks much for sharing this and for all the detective work resurrecting the old conversion scripts. You're exactly right that these are essentially file conversions of existing files and I'd...

Gavin and Floris; Thanks much for this, it's great to hear that our intuition about which GATK CNV input files to use worked out. I've also been doing comparisons using...

Brent; Thanks for the help with this. I agree it's probably also not the parsing. It's possible there was 1 overlapping SNP; bcbio ends up throwing a lot at peddy:...

That would be helpful for me. I know the output is not especially useful, but in bcbio we often get not good enough data that goes in and would be...

Brent; I definitely hear what you're saying about design. Raising a consistent error is also cool with me, it's just hard to tell up front if a dataset will have...

Thanks much for the helping with debugging on this. Beyond the hash failure from Cromwell the other errors I get are all from the workflow itself due to not preserving...

Thanks for this help with the configuration. I'm not intentionally overwriting the global `filesystem`, but I don't have an explicit import of reference.conf. Do I need to have an import...

Chris, thanks for the idea. I tried this and unfortunately had the same issue. From the behavior it looks like http is working in that the files get downloaded, but...

Chris; Thanks for working on this and for the test case to iterate with. This example does work for me in the sense that it generates an md5sum, but also...

Is there a fix in the latest development for this issue? I'm still stuck on this so not sure if I missed something.