A snakemake pipeline to estimate resistome data (using bakta, deeparg and amrfinder) from metagenome assemblies
conda create -y -n bakta3.10 "python=3.10" "mamba>=0.22.1"
conda activate bakta3.10
mamba install -y -c conda-forge -c bioconda bakta snakemake
conda activate bakta3.10## Bakta downloader does not work
wget https://zenodo.org/record/7669534/files/db.tar.gz
tar -xzf db.tar.gz
rm db.tar.gz
amrfinder_update --force_update --database db/amrfinderplus-db/This is why I used to had a pb avec nextflow funcscan
snakemake -j1 --cores 10
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