Metagenome-QTL

Create the conda environment needed for running snakemake and gen_conf.py.

$ conda create --file environment.yml --name YOUR_ENV_NAME
$ conda activate YOUR_ENV_NAME

Generate a YAML file containing metadata concerning your shotgun sequence files.

$ python3 gen_conf.py PATH_TO_RAW_FASTQ/ > samples.yml

Edit the options in config.yml to fit your analysis. The project field is the path where your results will be written to. Options under the parts-enabled field control which parts of the pipeline to run.

Run the pipeline using the run_pipeline.sh wrapper script.

$ bash run_pipeline.sh [SNAKEMAKE_ARGS]

This script will automatically run the pipeline using SLURM when executed on the nioo0004.nioo.int master node. You can change the contents of slurm.yml to modify the behaviour of the scheduler if needed.