Carl Mathias Kobel

fam-substrate-mapping.tsv missing

2

Using latest biconda release (4.1.4) Just downloaded a fresh database. When running, it seems like "fam-substrate-mapping.tsv" is not present in the database dir. I copied "fam-substrate-mapping-08252022.tsv" and everything looks to...

Hello, I'm looking for documentation of the inner workings of panito for use in scientific writing. Does any reference exist? Kind regards, Carl

Hi Takuya Aramaki I think many people would like to use the conda environment manager to install the dependencies for KofamScan. As a convenience to these users, I have created...

Use newer uniref 100 database for kegg calling

4

According to the checkm2 paper, the current version may be as old as from 2018?

`comparem2 --config input_proteins="path/to/my/proteins_*.faa" --until protein_tools` Or the workflow just automatically puts it in where there are .faa reading rules. Could be really cool to have for proteomics applications.

Upgrade to snakemake 8

1

No strong arguments other than just wanting to stay fresh. https://snakemake.readthedocs.io/en/stable/getting_started/migration.html

This issue is not part of the code base or this git repo, but I just want to use the github milestone system to keep track of the task. -...

Report v3 progress

3

Almost all is done, but some things are missing - [x] mlst - [x] abricate - [ ] fasttree/quicktree on core (consider skipping) - [ ] bakta (just copy-paste prokka)...

Continuous integration with some testing?

5

Running a few tests. - [x] Installing, both with conda and apptainer - [x] Downloading databases. - [ ] Running a few tests and checking that everything is produced correctly:...

For paper Against - [ ] Tormes - [ ] VEBA - [ ] Nullarbor - [ ] Anything else? Benchmarks must be for complete pairwise tools.