• Not recommended to hard-code files within snake file
• Can organize sample names, file paths, and software parameters in a YAML configuration file
• YAML - serialization language that transforms data into a format that can be shared between systems
• With snakemake, configuration file is a reference for the workflow

Running Snakemake with Config File

Snakefile - file.smk, contains rules for snakemake

snakemake -c 1 -s variant-yml.smk --configfile config_variant.yml

• –configfile – directing snakemake to a config file -c number of cores -s needed if using a named snakefile

Reproducible Environments

Snakemake supports reproducible environments

Example with Conda:

rule fastqc: input: “reads.fastq” output: “qc.html” conda: ”~/.conda/envs/fastqc_env” #path to conda environment

 shell:        "fastqc {input}"

Benefits: Easy dependency management, portable workflows

Can also create a environment.yml file, list conda envs and what to install

Snakemake with Conda Environment

module load miniforge
conda create
conda activate
snakemake command
screen/tmux

Keeps session running when disconnected

Can create different conda environment for different rules

Smakemake and containers

rule align: container: “docker://biocontainers/bwa”

Advantages:

• identical software environments
• portable across HPC systems
• easier collaboration