This repository is based on the Snakemake tutorial and PaneucalyptShortReads

The easiest way to setup these prerequisites is to use the Miniconda Python 3 distribution.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh

Creating an environment with the required software

$ conda env create --name snakemake-tutorial --file condaenv.yml

Activate the enviroment using:

$ conda activate snakemake-tutorial

Check enviroments

conda info --envs

Delete enviroment

conda remove --name myenv --all

NOTE: the data directory is generated by the workflow (common rule).

get dag.svg and check rules (see --dag -npr)

snakemake --dag -npr -j -1 | dot -Tsvg > dag.svg
eog dag.svg

Run complete Workflow

snakemake  -npr -j -1

utils/check_config.py allows you to read and print the config files:

from utils.check_config import *
config = readconfig('config.yml')
pconfig(config)
config['qc']

utils/check_metadata.py allows you to print the metadata generated at the common rule:

python utils/check_metadata.py