Hi,

Thanks for developing and the continuous improvements on Wakhan!

We currently have Wakhan incorporated in our nf-core style Nextflow pipeline: https://github.com/IntGenomicsLab/lrsomatic which supports ONT/PacBio (optional Fiber-seq) data and both tumor-only or TN paired.

Now we saw that you have made some updates, resulting in two modules hapcorrect and cna. I also saw that you have developed a nextflow pipeline as well to process long-read WGS data and where, in short, you do:

1. Alignment
2. Germline variant calling
3. Wakhan hapcorrect
4. Severus
5. Wakhan cna

I was now wondering what the reasoning and added benefit for hapcorrect is and if you do recommend us to also change our pipeline to include this step.

Best,
Luuk