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

nf-core

Does anyone (else) systematically convert their oncoanalyser output to cbioportal? we've developped a nf pipeline for it (amongst other data sources) and I just want to see if it's worth nf-core-ising it. :grin:

Hi Justin! Curious to hear what you convert and for what purpose ?

Ooooh yes please. I was just talking to the InPred team in Oslo on how we could use <https://github.com/tidywf/tidywigits> to also generate cBio inputs.

Not sure it fits the nf-core mold but we're starting to collect oncoanalyser-adjacent tools.

<@U09C2H24KFF>  A community supported cBioPortal loader would be great. Would be interesting to see how you get all the more WGS specific features in their model

<@U06MQLLLC2C> there was a lot of interest from oncologists in our research center to have a cbioportal instance for mainly research purposes, and currently processes both AmpliSeq gene panels + clinical data &amp; oncoanalyser WGS + clinical data for old and new patients into cBioPortal pretty regularily.

i'd also be curious to see if it fits the nf-core mold, seems like there would be many data input formats to consider.

<@U09C2H24KFF> had a look at the code and looks nice, any thoughts/plans to also include the _GenomeNexus_ annotation step? (or did I miss this ?)

And do you have a sense which oncoanalyser versions you are supporting (or how you would want to handle output format changes over time)?

<@U06MGLV91SS> in all honesty this is the first time i've heard of GenomeNexus. Seems like a natural fit, thanks for the heads up.

<@U071EDH97J5> in a perfect world we would like to stay up to date with the latest stable versions of oncoanalyser output formats