snakemake
Link to section 'Introduction' of 'snakemake' Introduction
Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
For more information, please check its website: https://biocontainers.pro/tools/snakemake and its home page: https://snakemake.readthedocs.io/en/stable/.
Link to section 'Versions' of 'snakemake' Versions
- 6.8.0
Link to section 'Commands' of 'snakemake' Commands
- snakemake
Link to section 'Module' of 'snakemake' Module
You can load the modules by:
module load biocontainers
module load snakemake
Link to section 'Example job' of 'snakemake' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Snakemake on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=snakemake
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers snakemake