cfsan-snp-pipeline
Link to section 'Introduction' of 'cfsan-snp-pipeline' Introduction
The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
Docker hub: https://hub.docker.com/r/staphb/cfsan-snp-pipeline
Home page: https://github.com/CFSAN-Biostatistics/snp-pipeline
Link to section 'Versions' of 'cfsan-snp-pipeline' Versions
- 2.2.1
Link to section 'Commands' of 'cfsan-snp-pipeline' Commands
- cfsan_snp_pipeline
Link to section 'Module' of 'cfsan-snp-pipeline' Module
You can load the modules by:
module load biocontainers
module load cfsan-snp-pipeline
Link to section 'Example job' of 'cfsan-snp-pipeline' 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 cfsan-snp-pipeline on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cfsan-snp-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cfsan-snp-pipeline