Nils Homer

#27

@kockan the intention is to have the command line options to match `grep` as much as possible, with no conflicts with bioinformatics-specific options (e.g. `--reverse-complement`). So the usage is very...

I this is a perfectly reasonable request with one caveat: if folks are providing multiple pairs of FASTQS (e.g. `S1.R1.fq.gz`, `S1.R2.fq.gz`, `S2.R1.fq.gz`, `S2R2.fq.gz`, ...) then I'd suggest you get only...

#30

Thank you for this write up! I am very familiar with this route, and understand the desire to make “using Snakemake to build my conda environment”. I don’t want to...

@johanneskoester is this as simple as having an option to skip conda environment creation and just use the directive as the environment name in `conda.Env`?

@johanneskoester Looking at the code and thinking about this more, I think we should have a sub-class of `conda.Env` that when given a path to a conda environment directory, does...

@johanneskoester I think reproducibility is the aim of what I am doing. I think that using Snakemake for reproducibility isn't always the right answer. Adding a linter warning is fine...

Also, what if we need to post-install things into the conda environment. A good example is `gatk3` (`gatk3-register GenomeAnalysisTK.jar`), or our own internal custom python code base. They both need...

The reason we (I am not alone, and implicitly represent a number of very large organizations) built/used extra infrastructure around doing conda env builds include, but is not limited to:...