Dear @Rike Hanssen @Maxime Garcia, I am the developer of VarNet somatic variant caller (https://github.com/skandlab/VarNet). I have made a pull request to add VarNet to nf-core/sarek here https://github.com/nf-core/modules/pull/11787 Kindly let me know if it looks ok! Thank you -Kiran

Made a comment on the module. Looking good, only issue I can see is handling the versions, we are migrating to topics instead of a versions.yml file

Thanks @Maxime Garcia I have modified the pull request. I have removed tbi since the module only outputs vcf.gz file (no tbi) at the moment. I will generate the tbi index file in a future release. Is that ok?

yeah no problem, we can always use tabix for this for now

Are you planning on having the tool on bioconda?

@Simon Pearce I have responded to your comments on github. I will add VarNet to bioconda when I find the time.

You'd need to make a PR to add it to sarek, alongside the other variant callers

@Simon Pearce I've made a PR: github.com/nf-core/sarek/pull/2303

I would suggest all three of these should be fixed in your next release of varnet:

• VarNet writes its VCF with plain gzip, which tabix cannot index. The output is recompressed as BGZF and indexed with

htslib/bgziptabix

.

• VarNet only accepts BAM, so

varnet

is added to the tools that trigger CRAM-to-BAM conversion in

workflows/sarek.nf

.

• VarNet is excluded from

--normalize_vcfs

,

--filter_vcfs

and

--snv_consensus_calling

. Its VCF header declares neither contigs nor the `DP`/`RO`/`AO`/`AF` INFO fields it writes, and bcftools refuses to write such records as BCF, which

bcftools sort

does internally. A VarNet release with a complete header is planned, after which the exclusion can be lifted.

And ideally you make that release first 😉

@Simon Pearce @Maxime Garcia Could you please approve this PR: github.com/nf-core/modules/pull/13147 I will then update the PR to sarek. Thanks : )