This is a snakemake pipeline to process Illumina short-reads and perform SV with Delly
- Programs are listed in the conda environment in
workflow/envs/environment.yaml
, it can be used to create a local environment or allow snakemake to create them with--use-conda
- Inputs are the Fastq files and a reference genome, all specified in a
config.yaml
file - Output directory is specified with the
-d <dir>
parameter for snakemake - The pipeline can be run in a cluster if it is configured
samples:
- sampleID1
- sampleID2
fastq_dir: /path/to/fastq/dir
genome: ref/genome.fa
snakemake --configfile <your-config.yaml> -d <output_dir>
Juan Caballero (C) 2024