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:

├── 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


For checking workflow and debug

snakemake -np

Visualise the workflow

snakemake --forceall --dag | dot -Tpng | display

Indices and tables