Collective Snakemake workflows for easy and reproducable NGS data analysis.
Workflows may contain modified parameters, Please look at snakemake
files before use.
Currct workflows
Workflows are making in progress. I will add more downstreem tools as go along.
You have an workflow in mind too add! Requet it here -
You need to have Python3 installed in your system with conda
enabled.
Install needed tools with following command
conda env create -f environment.yml
conda activate snakeflows
Downlorad sample data to test the workflow:
wget https://www.dropbox.com/s/bnvjbhq4970pvg8/sample_data.tar.gz?dl=0
Before you run write_sample_to_json.py
, samples directory arangement and it's naming needs to be proper such that it can be read by the script and call furthere in snakemake
files.
Something like this:
samples
├── SET1_dummy
│ ├── SET1_dummy_R1.fastq.gz
│ └── SET1_dummy_R2.fastq.gz
└── SET3_dummy
├── SET3_dummy_R1.fastq.gz
└── SET3_dummy_R2.fastq.gz
This will be used to automatic detect samples names and call them in snakemake
files.
python3 write_sample_to_json.py --fastq_dir full_path_to_samples_directory
First Edit the config.yml
files inside workflow directory with required full paths.
Then simply call snakemake
from workflow directory (With additional parameters if required)
snakemake --cores 12
For checking workflow and debug
snakemake -np
Visualise the workflow
snakemake --forceall --dag | dot -Tpng | display
Upcoming additons: