smk_stacks_workflow

RADseq workflow built around STACKS full-parallelized and automated using SNAKEMAKE

Installation

Prerequisites

• python3
• snakemake
• singularity

Singularity/Docker container

Pull the container to your machine

singularity pull --name gbs_workflow.sif shub://Grelot/smk_stacks_workflow:gbs_workflow

Check if the container is working well

singularity run gbs_workflow.sif

should output

Opening container...ubuntu beaver: STACKS 2.5, Trimmomatic 0.33, bwa-mem 1, bwa-mem 2, samtools 1.10, vcftools 0.1.15, bedtools 2.26.0

Example of use: running stacks2 from the container

singularity exec gbs_workflow.sif gstacks --version

should output

gstacks 2.5

Data files

Illumina paired-end fastq files must be stored into a folder:

.
└── FastqFolder
    ├── runA_R1.fastq.gz
    ├── runA_R2.fastq.gz
    ├── runB_R1.fastq.gz
    └── runB_R2.fastq.gz

Configuration

• Snakemake will use information stored into a configuration file in order to run the workflow.
• You have to modify 01_infos/config.yaml to configure your own workflow.
• A complete description of the configuration file is available on this wiki page.