This tool wraps metagenomic workflows. Why? Because there are already lots of well-written workflows out there, but depending on your use-case neither of them can single-handedly do all the things you want.
Therefore ductape
takes advantage of how Snakemake can integrate both
foreign
and native
workflows. The idea is to extend the functionality of existing workflows without
adding yet another one to the mix.
- Install with
conda create -c bioconda -n ductape ductape
and activate the environment. - Run
ductape init pipelinedir
and change into the newly created directorypipelinedir
. - Edit
ductape.yaml
andsamples.csv
. - Run
ductape run
.
- Clone this repository with
git clone [email protected]:NBISweden/ductape.git
- Change directory:
cd ductape
- Set up a conda environment to use for installation:
conda create -n ductape python
- Activate the environment:
conda activate ductape
- Install the package:
python -m pip install .
So far ductape
wraps the nf-core/mag
workflow and extends it with eggNOG
annotations for each assembled group of samples.