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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`