Ideally the only required software to run the pipeline should be Nextflow and Docker/Singularity. I would suggest review the installation instructions, requiring a conda env. shouldn't be required.

[jhayer]

No description provided.

[mberacochea]

Hi! Thank you for the changes; I think they are a great improvement.

I understand the usefulness of https://github.com/jhayer/baargin/blob/main/download_db.py, but this is the main reason for the requirement of a Conda environment. By also providing a set of curl or wget commands, it would be possible to make the Conda environment not required. The most technically savvy users will probably notice this. I feel that not having a Conda environment makes using the pipeline more accessible, especially for Nextflow users.

For plasmidfinder_db , it's possible to download the repo using the Bibucket Download Repo URL: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/314d85f43e4e.zip.

Something like:

mkdir dbs/plasmidfinder
cd dbs/plasmidfinder
wget https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/314d85f43e4e.zip -O plasmidfinderdb && unzip -j plasmidfinderdb.zip

[jhayer]

Hi ! Thank you for the comments.
We had actually added a "manually" section to the documentation for the databases download (using wget, curl or git clone).