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

nf-core

New release is out :christmas_tree:: <https://github.com/nf-core/sarek/releases/tag/3.7.0> supporting now 2 new tools:

• :hourglass_flowing_sand: Filtering of variants with `bcftools filter` : by default `-f PASS,.`
•  :handshake: Consensus calling with `bcftools isec` : variants called in n number of callers
• Various bug fixes for BBSplit that was added in `3.6.0` 
We now have two paths for post-variantcalling processing: variants can either be processed with Varlociraptor or go through a `filter -&gt; normalize -&gt; intersection` path way. Either path then flows into annotation.

We found a bug when running single-sample haplotypecaller. We are looking into it right now, but since I am technically out it might be next week until we get to push a patch release

Cross-posting this here in case it is relevant - I spotted some weird bbsplit problems in my own pipeline aftering updating bbsplit to the latest version: <https://nfcore.slack.com/archives/CE8SSJV3N/p1765213014112749?thread_ts=1764240778.280839&amp;cid=CE8SSJV3N>

And congrats on the new release!

:sadpanda: probably the same then since we just use the shared module

New release is out <https://github.com/nf-core/sarek/releases/tag/3.7.1> with:

• Fix Haplotypecaller failure on 3.7.0 in <https://github.com/nf-core/sarek/pull/2069|#2069>
• Module updates:
    ◦  MultiQC (1.31 -&gt; 1.33; adds BBsplit reporting) 
    ◦ BBSplit (bug on shared file systems, see above) in <https://github.com/nf-core/sarek/pull/2073|#2073>
• Fix to validate `umi_read_structure` in <https://github.com/nf-core/sarek/pull/2071|#2071>
