Usage

Selscape provides two modes: testing mode for learning the workflow with example data, and main analysis workflow for analyzing your own datasets.

Testing Mode

1. Configure for Testing

Ensure testing_mode: true in your main configuration:

# config/main.yaml 
testing_mode:  true

2. Run Test Analysis

The repository includes small example datasets (YRI and CHS populations, chromosomes 21-22) in examples/data/Human/, so you can start testing immediately:

# Local execution 
snakemake --cores 1

# HPC execution 
snakemake --profile config/slurm/ --jobs 10

Main Analysis Workflow

1. Prepare your Data Place your raw VCF files in the correct directory structure:

resources/data/{species}/raw/
├── chr1.vcf.gz
├── chr1.vcf.gz.tbi 
├── chr2.vcf.gz 
├── chr2.vcf.gz.tbi
└── ...

2. Configure for Main Workflow

# config/main.yaml
testing_mode: false

species: "YourSpecies"

populations:
  - PopA
  - PopB

data:
  # Update paths to match your data structure
  vcf_files:
    base_path: "resources/data"
    file_prefix: ""
    file_suffix: ".vcf.gz"
    chr_name: "chr{i}"  # Adjust to match your naming

  metadata: "resources/data/YourSpecies_metadata.txt"

  chromosomes:
    - 1
    - 2
    # ... add all chromosomes

3. Run Main Analysis

Run Analysis on HPC:

snakemake --profile config/slurm/ -j 30

Run Analysis locally:

snakemake -j 5

Clean Restart

To start fresh (removes all previous results):

rm -rf resources/ results/ logs/

Basic Options

Command	Purpose
-j 30	Use 30 parallel jobs
--profile config/slurm/	Submit jobs to SLURM cluster
-n	Dry run (preview what will be executed)

For further information, please visit the Snakemake documentation website.