LukaP

Hi, to my knowledge fastp doesn't handle this case, thus I made a custom tool some time ago to generate fastqs with the UMIs in the headers, in the same...

Hi, I updated the readme with install instructions and added a pre-compiled bin for linux in the repo.

I have a very similar issue here with the following traceback : ```py Traceback (most recent call last): File "/dev/envs/shared/pipeline/lib/python3.10/site-packages/snakemake/sourcecache.py", line 330, in __init__ os.makedirs(self.cache, exist_ok=True) File "/dev/envs/shared/pipeline/lib/python3.10/os.py", line 215,...

I'm pretty sure the SNAKEMAKE_OUTPUT_CACHE has nothing to do with the runtime cache where the error is raised, as it is used to cache common results from rules between workflows....

I managed to fix the issue with something that looks completely unrelated. Working on a cluster with slurm, my drmaa string included `--mem-per-cpu={cluster.mem}` Switching this to `--mem={cluster.mem}` and adapting the...

What is you launch command ? The error is telling you that you are using mutually exclusive arguments to sbatch. What did you put after `--drmaa` ?

Okay so the issue is probably in your profile file, check out either the parameters for your rule or the default parameters and remove one of --mem, --mem-per-cpu, or --mem-per-gpu

@moritzschaefer The *probably* correct workflow here is to separate your development process from the production. So, one folder where you basically have main + develop and stay on develop. Once...

> Which `rule a` is this referencing? : Well, `rule.a` is referencing the only rule that is in scope, aka the one defined in `main.smk`. Thanks for providing an option...