[FEATURE] Tumor mutational burden (TMB) scoring

[apeltzer]

nf-core/sarek feature request

Is your feature request related to a problem? Please describe

TMB / tumor mutational burden is a key metric for many oncology related projects and thus could be a feature requested by many users of the pipeline at some point to be computed similar to MSI status (which is already done in the pipeline).

Describe the solution you'd like

Have some method / way of computing TMB status and reporting this to the user in the main MultiQC table ideally.

Describe alternatives you've considered

[apeltzer]

Easy to use feature would be this here: https://github.com/bioinfo-pf-curie/TMB

[apeltzer]

A good explanation how to do the job potentially as this evaluates several panels + WES that could be of interest: https://www.nature.com/articles/s41598-020-68394-4

[apeltzer]

potentially worth looking at too: https://github.com/bcgsc/TMBur

[apeltzer]

Also a good tool apparently, estimating TMB: https://github.com/bioinform/ecTMB

[apeltzer]

Strong tendency towards using the curie approach because:

• conda recipe --> biocontainer in place ✔️
• good examples / documentation in place ✔️
• straightforward output for multiqc (tsv tables are produced automatically --> could just report this in separate table in MultiQC report in Sarek) ✔️

All these points above are sometimes hard to achieve if you have to do them yourself --> good idea to rely on this instead 👍🏻

[maxulysse]

* straightforward output for multiqc (tsv tables are produced automatically --> could just report this in separate table in MultiQC report in Sarek) heavy_check_mark

MultiQC module possibility even?

[FriederikeHanssen]

Hey! I started looking into this. I actually can't find the curie tool on anaconda.org. From the README I think, they provide an environment file to set up, in which then the python scripts can be run. then also no biocontainers would exists. Did you find anything else @apeltzer ?

[apeltzer]

No, nothing else - I suspect that they have their own conda channel where they provide everything this uses / needs.

[nservant]

Hi there, just be in touch with @FriederikeHanssen !
So indeed, there is no conda repo, just because I'm not familiar with making such package :)
But we'll be happy to do it of course !