Lucas Czech

Hi Gabi, thanks for using grenepipe, and happy to hear that you find it useful! Yes, generally Snakemake will work fine if you delete files that are not needed by...

I'm having the same issue (and was preparing a bug report already, before I found this one). Bump on fixing this :-) Edit: See also https://github.com/snakemake/snakemake/issues/3191

Hi Homère, if you are working with single end reads, only `fq1` should be filled, not `fq2`. See [here](https://github.com/moiexpositoalonsolab/grenepipe/wiki/Setup-and-Usage#samples-table) for details. I'd recommend running the script to automatically generate the...

Hi @Karimelakoum, yes, the removal is activated by default because in a typical run of grenepipe, as far as I can tell, duplicates are not used downstream anyway, so it...

Hi Karim, thanks for the links! Hm, do you think it would make sense to change the default in grenepipe then? I am however not sure about the implications for...

Hi Eric, thank you for raising these questions and for reporting your experience with the tools on your data! Those are good points worth investigating (for your sake, and for...

Hi Eric, thanks for the details! Nothing there that jumps out to me as a potential cause for the discrepancies you are observing. So I guess this needs a bit...

Hi @Song-10-YF, what exactly do you mean by "BAM files for multiple populations of a species"? How were those files produced exactly? Generally, the idea of Pool seq is to...

Hi @Song-10-YF, any updates on this? Cheers Lucas

Hey hey! I assume this is resolved? If not, feel free to re-open or start a new issue :-)