Lucas Czech

Dear @bioinfowheat, thanks for the positive feedback, happy to hear that the tools is useful :-) On the `dev` branch, I have now implemented an option in the `fst` command,...

Hey @bioinfowheat, just wanted to give a quick heads-up about the latest release [grenedalf v0.5.0](https://github.com/lczech/grenedalf/releases/tag/v0.5.0). This now finally implements a re-designed approach to the whole filtering and dealing with missing...

Hi @JudithNeukamm, thanks for the follow up. Unfortunately, I did not yet get back to that project, so as of now, I don't know whether that solution works. I'll post...

Hey Meixi, thanks for reporting this! Yes, with grenepipe v0.13.0, we moved to a newer snakemake, which uses a different mechanism to run on slurm, and I have not fully...

Ah nice, yes, that makes sense. I see some interesting changes you made: - slurm config fixes - `--not-recursive` option for the generate table script - new `all_trims` shortcut rule...

Hey @meixilin, thanks again for reporting this. I've fixed the profiles issue now, it will be part of the next release v0.13.3, or on the master branch now. Also, I...

Hey Yannick, so, you installed the grenepipe env via micromamba, then activated it, and then ran snakemake from within that environment? What are the exact commands that you are running...

Haha no worries, it happens :-)

Okay, interesting, a lot is going on here... First, the error was in sample `B-1`, not `D-1`. Could you maybe also send me the file `logs/mapping/bwa-mem/B-1.log`? Furthermore, the error message...

Hej Yannick, > unfortunately no log seems to have been created for B-1, I added the only one in the bwa-mem log folder. Ah okay, that likely means the job...