Matin Nuhamunada

Use this approach to speed up emapper in large batch: https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#user-content-Setting_up_large_annotation_jobs

Hi @ChMaWh, here is the first draft of `defense-finder` subworkflow: ## Usage: 1. Create a conda environment and install the [`BGCFlow` python wrapper](https://github.com/NBChub/bgcflow_wrapper) : ```bash # create and activate a...

It seems the latest python release cause error when reading the config resources, pinning the python to 3.11 fix the issue ``` DEBUG 05/10 10:32:05 Starting new HTTP connection (1):...

Using pandas 2,1,0 and above cause this unnecessary warning: ```python /data/a/matinnu/bgcflow/workflow/rules/common.smk:369: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value...

Can we containerize the workflow? Separate databases (resources), workflow, and output+logs with [podman](https://podman.io/) maybe?

Prune BGCFlow rules

1

I think we should reduce the number of rules, either by: - Dropping unused or redundant rules - Merging relevant rules into one package These are the rules that are...

Hi, is it possible to update the conda environment used in the github action? I think the current action uses `peppy=0.34.0`. I would like to update it to `0.35.1`

Pandas frame.append method is deprecated

2

Hi, thanks for the nice tool here :) When running `peppy.Project(project_config_file)`, I keep getting this warning: ```bash /home/matinnu/miniconda3/envs/snakemake/lib/python3.10/site-packages/peppy/project.py:103: FutureWarning: The frame.append method is deprecated and will be removed from pandas...

Hi, I'm quite new to DBT and DuckDB. I'm still a bit confused about setting up primary and foreign keys in the models. I saw that this is how it...