bgcflow_wrapper

A snakemake wrapper and utility tools for BGCFlow.

Usage

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Clone this repository:

git clone [email protected]:matinnuhamunada/bgcflow_wrapper.git

Use conda/mamba to create environment and install the package:

cd bgcflow_wrapper
mamba env create -f env.yaml
cd ..

Developer Note: BGCFlow wrapper are still in development phase. We will make it available to install using pip when BGCFlow wrapper is released.

Features

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$ bgcflow_wrapper

Usage: bgcflow_wrapper [OPTIONS] COMMAND [ARGS]...

  A snakemake wrapper and utility tools for BGCFlow
  (https://github.com/NBChub/bgcflow)

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  clone       Use git to clone BGCFlow to local directory.
  deploy      [EXPERIMENTAL] Deploy BGCFlow locally using snakedeploy.
  get-result  Use rsync to copy a given project results from BGCFlow.
  init        Create projects or initiate BGCFlow config.
  rules       Get description of available rules from BGCFlow.
  run         A snakemake CLI wrapper to run BGCFlow.
  serve       Run a simple http server of the output directory.

Tutorial

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# activate the environment
conda activate bgcflow_wrapper

# get a clone of BGCFlow in your local machine
bgcflow_wrapper clone MY_BGCFLOW_PATH #change PATH accordingly

# initiate an example config and projects from template
bgcflow_wrapper init --bgcflow_dir MY_BGCFLOW_PATH

# do a dry-run
bgcflow_wrapper run -n --bgcflow_dir MY_BGCFLOW_PATH

# find out available rules
bgcflow_wrapper rules --bgcflow_dir MY_BGCFLOW_PATH

# get description of a rule
bgcflow_wrapper rules --describe query-bigslice --bgcflow_dir MY_BGCFLOW_PATH/

# get citation of a rule
bgcflow_wrapper rules --cite query-bigslice --bgcflow_dir MY_BGCFLOW_PATH/

Generating BGCFlow projects from Jupyter Notebooks

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You can also generate new projects from Jupyter notebooks:

from bgcflow_wrapper.projects_util import generate_project
import pandas as pd

df_samples = pd.read_csv('samples.csv', index_col=0)
description = "Project generated from notebook"

generate_project("BGCFLOW_PATH",
                "MY_PROJECT",
                use_project_rules=True,
                samples_csv=df_samples,
                prokka_db="prokka-db.csv",
                gtdb_tax="gtdbtk.bac120.summary.tsv",
                description=description
                )

Credits

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This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.