Silas Kieser

Does the new resource: tmpdir go in this direction?

Ok. We should run snakemake as a job on the cluster system where it has access to a `/scratch` . However snakemake still creates the shadow rule multiple times. Is...

I think the latest version os snakemake define a `resources.tmpdir` which you can use in your rule. You can then define the tmpdir as comand line argument to snakemake `...

no shadow prefix and tempdir are two different aproaches.

No response from the developer since three years is probably to be interpreted as a No.

We would need the original alignments, that's all..

Answer: The PhiX reference will be automatically downloaded. The `host_genome.fasta` Should be in the default directory if you ran the `setup_codespaces.sh` The ide is to move the host_genome.fasta into the...

By the way, I'm giving a course on metagenome atlas https://oulu.fi/uniogs/node/212131 If you want and can attend. try to register. For the error check what's in `sample2/logs/assembly/pre_process/error_correction_QC.log` If it's the...

Probably no. I am not shure if you can do the assembly. You would pool the 3 replicats, would you? But you can always try. Maybe with megahit.

Check the log: sample2/logs/assembly/pre_process/error_correction_QC.log If it's due to the memory increase mem in the config file to 100