Friederike Hanssen

> ing this error but I've added '0' in the 'status' column on my csv input (bam, step variant_calling) The error mesage is likely a false flag. We are already...

@DimitrisZisis internally propagated and someone will fix the slack link. Sorry about that. There is a amazon-healthomics channel on slack that would be a good place to ask.

Slack link was fixed

Did you press 'Join' in the top right corner? https://nf-co.re/

@mribeirodantas can you check what is going on there?

What version are you running? Can you send the error message? there are several issues with dragmap that were never resolved: https://github.com/Illumina/DRAGMAP/issues/47

Hey! Yes this is due to the intervals file that is used. We use the one provided by GATK. You can change the intervals file or skip the intervals usage...

I need to read up on it a bit more. We basically just took the reference files as is from GATK and ran with it: https://gatk.broadinstitute.org/hc/en-us/articles/360035889551-When-should-I-restrict-my-analysis-to-specific-intervals So I am guessing...

Hey! When you run tiddit manuallly (outside of sarek) on the problematic samples, does it finish and terminate?

oh yeah the thread thing is definitely an oversight and we need to fix this on module level. You could add it by setting a custom config and adding there...