Running Snakemake

To run Snakemake, there are four parameters to keep in mind. First of all, if you're unsure about having set up everything correctly, try a dry run. Dry runs show only the rules that are planned to be run:

snakemake -n

If you're getting a list of rules starting with Job counts, the settings are fine. Snakemake requires you to specify the maximum number of cores/threads that the workflow should use. This can be set using the -j or --cores parameters. For example to run Snakemake with 1 core, use:

snakemake --use-conda -j 1

or

snakemake --use-conda --cores 1

Finally if you installed Singularity, you can run ARPEGGIO in a container to further ensure reproducibility as follows:

snakemake --use-conda --use-singularity

Next section

5. Output structure

Wiki index

Basic steps to run & get an idea of the workflow:

1. Overview
2. Input files
3. Configuration file
4. Running Snakemake
5. Output structure

Advanced information to better understand & modify the workflow:

6. Snakefile (rules and relationships)
7. Scripts
8. Software and tools