Skip to content

3. Running the Pipeline

3.1 Pipeline Overview

The Snakemake workflow has a multiple options: 

Usage:
    ./run -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>

    Required Arguments:
    1.  RUNMODE: [Type: String] Valid options:
        *) init : initialize workdir
        *) run : run with slurm
        *) reset : DELETE workdir dir and re-init it
        *) dryrun : dry run snakemake to generate DAG
        *) unlock : unlock workdir if locked by snakemake
        *) runlocal : run without submitting to sbatch
    2.  WORKDIR: [Type: String]: Absolute or relative path to the 
        output folder with write permissions.

3.2 Commands explained

The following explains each of the command options:

Preparation Commands

  • init (REQUIRED): This must be performed before any Snakemake run (dry, local, cluster) can be performed. This will copy the necessary config, manifest and Snakefiles needed to run the pipeline to the provided output directory.
  • dryrun (OPTIONAL): This is an optional step, to be performed before any Snakemake run (local, cluster). This will check for errors within the pipeline, and ensure that you have read/write access to the files needed to run the full pipeline.

Processing Commands

  • runlocal - This will run the pipeline on a local node. NOTE: This should only be performed on an interactive node.
  • run - This will submit a master job to the cluster, and subsequent sub-jobs as needed to complete the workflow. An email will be sent when the pipeline begins, if there are any errors, and when it completes.

Other Commands (All optional)

  • unlock: This will unlock the pipeline if an error caused it to stop in the middle of a run.
  • reset: This will DELETE workdir dir and re-init it

To run any of these commands, follow the the syntax: 

./run --runmode=COMMAND --workdir=/path/to/output/dir

3.3 Typical Workflow

A typical command workflow, running on the cluser, is as follows: 

./run --runmode=init --workdir=/path/to/output/dir
./run --runmode=dryrun --workdir=/path/to/output/dir
./run --runmode=run --workdir=/path/to/output/dir

3.4 Passes explained

MAPLE is to be run in three Passes: 1.) first_pass completes trimming, alignment, assembly and a complete histogram 2.) second_pass completes subsetting, DAC analysis and DYAD analysis 3.) third pass completes comparisons between multiple samples