Usage

After the setup, you are ready to run the pipeline on your specific files and use-cases. Generally, the execution follows the same principles as defined in the snakemake documentation. However, here is a quick overview about the basic commands for execution, since they slightly differ depending on the chosen mode of the setup:

In general, the classic setup needs to be run using --use-conda to tell Snakemake to build and use the rule-specific envs.

Exemplarily for both, a dry-run can be executed as follows:

Classic:

   snakemake --use-conda -n

Alternative:

   snakemake -n

Tip

If you run into problems with mamba or conda not being able to create the rule-specific environments on the go, you might first need to allow conda or mamba to be able to call subprocesses. Check out this as a starting point.

Example commands

To illustrate the order of execution for these rules in a directed acyclic graph, run:

   snakemake --forceall --rulegraph | dot -Tpng > dag.png

To run the full pipeline using 20 cores and automatically generate a report about the run afterwards, run:

   snakemake --cores 20 && snakemake --report myreport.html

This, however, will fail since the sample names defined in the default config are dummies. Let's look at the tutorial for a step-by-step explanation of the the workflow and its outputs.