RADseq workflow built around STACKS full-parallelized and automated using SNAKEMAKE
- python3
- snakemake
- singularity
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
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
- 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.