Efi Kontou

I have first created the environment: `conda env create --prefix ".snakemake/conda/envname" -f "workflow/envs/requirements.yaml" ` Example rule: ``` rule example: input: "results/Interim/input.tsv" output: "results/Interim/output.tsv" conda: ".snakemake/conda/envname" shell: """ mv {input} {output}...

If I don't create the env using a prefix it should work, but I want it in my .snakemake/conda path. I guess this is more of a conda limitation regarding...

This works. Can you merge the changes? @johanneskoester

Actually I am dealing with the same issue when I use OpenMS 3.0 (build version) with Sirius < 5.0 (specifically 4.9.15). `Error: Unexpected internal error (Sirius was executed, but an...

@chrisburr It would help a lot if you could accept this PR :)

Yes you do, when it finds matches to the spectral libraries (pubchem, etc). Example output from SiriusAdapter using CSI: [structures_Epemicins.csv](https://github.com/OpenMS/OpenMS/files/8304643/structures_Epemicins.csv)

ah I see! No idea if this is possible.

One small comment: I would set the default compound+tree timeout to 100 (s) instead of infinite (-1), otherwise Sirius runs for a day for very simple files (If you have...

FeatureFinder and MetaboAdduct decharger are really fast, at least with my samples (which are quite complex). I have now run their workflow (actually using docker is a super good idea...

Ok here are the stats so far for 3 identical files, using 3 cores in my Mac: OpenMS (snakemake) 1. FeatureFinderMetabo -in {input} -out {output} -algorithm:common:noise_threshold_int "1.0e04" -algorithm:mtd:mass_error_ppm "10.0" -algorithm:epd:width_filtering...