Lucas Czech

Howdy! Your repeated inquiry shall indeed be forgiven, as I did in fact say I was going to work on it this summer, which technically leaves me 5-ish days... but...

Hi @ospfsg, The first issue you mention (https://github.com/snakemake/snakemake/issues/2957) can likely be ignored, as that is some Snakemake-internal warning, but does not seem to affect the runs. The second one is...

Hi @ospfsg, the command should be the same, i.e., `--use-conda --conda-frontend mamba`. The way to get snakemake to use micromamba is by using micromamba to install the grenepipe environment, activate...

Hi Octavio, is this issue solved then, given the new issue in #58? Let me know if we can close this, or if you have further questions :-) Cheers Lucas

Okay, I assume we can close this then :-) If not, as always, feel free to comment, re-open, or start a new issue! Cheers Lucas

Hi @RvV1979, thanks for reporting this, that seems to be a consequence of the changes in Snakemake concerning their SLURM setup. Similar issues were reported [here](https://github.com/moiexpositoalonsolab/grenepipe/issues/51). I think the cluster...

Hey @RvV1979, finally found the time to reproduce this error, and fixed it by updating the cluster config file for the new slurm executor. Will be part of the next...

Just ran into a similar, but slightly different variant of this while trying to format another file. Minimal example: ```snakemake if condition_1: include: "rule_1.smk" elif condition_2: pass else: raise Exception("Invalid...

Hi Alexis @alexis-sedg, interesting approach! Do you have a reference or link to that sub-pooling procedure? Why is that the recommendation for that variant caller? Yes, grenedalf can do that,...

Hi Alexis, thanks for the details! Hm, interesting approach - however, I am not quite sure that the following is true in general: > The intuition being that sequencing errors,...