Welcome to Snakflows’s documentation!¶
Workflows may contain modified parameters, Please look at snakemake
files before use.
Currct workflows¶
Quick start¶
1. Prepare samples directory properly¶
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
2. Generate samples.json
file¶
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
3. Run Workflows¶
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
Additional¶
For checking workflow and debug
snakemake -np
Visualise the workflow
snakemake --forceall --dag | dot -Tpng | display