Simon Pearce
Simon Pearce
@lbeltrame , looks like your blocker has been merged.
Yes, if you use the branch that Maxime linked to it then sentieon should work again.
@FriederikeHanssen , do you still have plans for this?
Added stub tests. We do have working tests in the modules directory, so in theory we should be able to get something working here.
To add a stub test, copy the test and add a line `options "-stub"` above the `when`. But the module itself is missing a stub, so that'd need adding too....
@LeonHornich , do you need a hand to finish this off?
Let's get this in.
I don't actually know how often a tarred file is used in the wild, whether it is only used for testing purposes because we can't stage a folder ;)
Hmmm, I implemented the samtools sort memory setting in my in-house pipeline last week...
Attached is a sam file showing the issue (set as .txt for github to upload) [all_a.sam.txt](https://github.com/user-attachments/files/21319556/all_a.sam.txt)