A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Dear all, thank you for your amazing work! I was looking at your pipeline and I was wondering if you have evaluated the possibility to integrate this pipeline as a workflow in nf-core/sarek. In this way a persona can choose to build the reference panel and automatically run sarek with one command. what do you think about it?

in my ideas, you'd need to run this pipeline on 40 normal samples to then run it on sarek and other downstream pipelines with the newly created panelreferences

In fact, in general, we are moving away from integrating reference computation with pipelines. It seemed useful at first but turns out it is a big maintenance overhead, you typically would only want to run it once and then reuse the references over and over again and share the references between different pipelines (see <#C073ZDLNC92|>)

and to be fair, pon aren't a different kind of references that the regular ones