Matthieu Muffato

I deleted the ones that are stale and are linked to pull requests merged or closed (most often because they were onto `master` and have been superseded with another one...

Oh, didn't realise there were that many ! Not too bad indeed. Here is my list of branches with a name that suggests an action could be taken. [`revert-*` ones](https://github.com/nf-core/test-datasets/branches/all?query=revert)...

Similar to https://github.com/sanger-tol/variantcalling/issues/93 perhaps ? Tyler wrote he could get it to work with Rosetta. I'm a surprised you're having an issue with gunzip. I'd have thought it's a standard...

The extra haplotypes are absolutely needed in MerquryFK for the k-mer stats. We can in fact run the whole GENOME_STATISTICS sub-workflow on those haplotypes to get some information. *If* HiC...

> My suggestion was to cat haps together like in EAR. ok ! > Or we put some dev time into MerquryFK in order We've got Gene with us for...

> I've just been advised we probably shouldn't cat the haps together. Having an amorphous haplotype statistic helps no one really. If we only use the hap1 and combined stats,...

Is it right to have these settings hardcoded in the module ? How does it interact with pipeline-level config file doing ``` withName BWAMEM2_INDEX { memory { ... } }...

I was more worried that 28 GB / Gbp is still too high in my view. I use 24 GB / Gbp in my pipelines and wouldn't want nf-core to...

FYI, I've just checked our LSF logs and there's been _zero_ memory failures over the 1,698 `BWAMEM2_INDEX` processes that we ran in 2024 with 24 GB/Gbp. The memory efficiency is...

> > The proposed implementation/purpose of -u amend is to create a copy of the pipeline that entirely relies on the external cache alone. That's why the local singularity-images/ directory...