Running the Pipeline
Running MAVIS using a Job Scheduler
MAVIS v3 uses snakemake to handle job scheduling and setup
The MAVIS pipeline is highly configurable. Some pipeline steps (cluster, validate) are optional and can be automatically skipped. The standard pipeline is far-left.
The most common use case is running the pipeline through snakemake
snakemake -j <MAX JOBS> --configfile <YOUR CONFIG> -s Snakefile
If you are submitting to a cluster, use the snakemake profiles
snakemake -j <MAX JOBS> --configfile <YOUR CONFIG> --profile <YOUR PROFILE NAME> -s Snakefile
This will submit a series of jobs with dependencies.
To use the mavis docker container through singularity, instead of installing mavis via pip, add the
--use-singularity
flag.
snakemake -j <MAX JOBS> --configfile <YOUR CONFIG> --profile <YOUR PROFILE NAME> --use-singularity -s Snakefile`