Usage

Running locally

Once configured, the workflow can be run using snakemake. Often, it is prudent to first test your configuration by performing a dry-run using:

snakemake --use-conda -n

If you are satisfied with your configuration, you can execute the workflow locally on $N cores using:

snakemake --use-conda --cores $N

Running on a cluster

You can also run the workflow in a cluster environment using:

snakemake --cluster qsub --jobs 100

Running in a different folder

If you want to run the workflow in another directory to avoid modifying files in the workflow, you can run snakemake in a different work directory as follows:

snakemake --directory ~/scratch

This assumes that the command ifself is run in the workflow directory, otherwise snakemake won’t find the Snakefile. The command can also be run elsewhere as follows:

snakemake -s ~/path/to/workflow/Snakefile --directory ~/scratch

Note that in both cases, ~/scratch should contain the appropriate config.yaml and sample.tsv files, as snakemake searches for these files in the work directory.

See the Snakemake documentation for further details on snakemake options.