Hello, I am using TNScope and was thinking of adding to the module so that it can handle tumor normal pairs as described here. Would that work?

sure 👍

Should I do a separate module? Maybe do the module on nf-core/modules and then include it here? It just seems to be a very different use case than the one on sarek at the moment

ideally the tnscope module can be extended to both. See for example mutect2. BUt in either case add to nf-core modules first and then into sarek

What exactly are you after? TNscope is currently implemented as a tumour normal caller?

Thanks @Simon Pearce! I have been in communication with Sentieon about my situation, and they suggested to use a different strategy:

For WES and WGS samples, we suggest using TNhaplotyper2 and TNfilter (with OrientationBias and ContaminationModel) instead of TNscope... We have found that TNhaplotyper2's filtering works very well with WES/WGS samples.

So I wanted to add that option to the module

do you know what the difference between tnseq and tnscope is?

From this: "TNscope® uses an improved variant calling algorithm to obtain higher accuracy and improved runtimes, while TNseq® matches the GATK's Mutect2 somatic variant calling with substantially improved runtime and parallelization."