Tips

Here are some tips for better understanding and troubleshooting that I found useful.

• always use the flag -p that makes Snakemake print the resulting shell commands that will be executed.

  snakemake -p

• always perform first a dry run using the flag -n, to check if the configuration works and the workflow does what you intend it to do.

  snakemake -p -n

• if unsure why a certain rule will be executed use option --reason during the dry run, this will give the reason for the execution of each rule.

  snakemake -p -n --reason

• if you use a module in multiple projects with different configuration files use the command line argument --configfile to overwrite values from the configfile statement. Important note from the docs: Note that any values parsed into the config dictionary with any of the above mechanisms are merged, i.e., all keys defined via a configfile statement, or the --configfile and --config command line arguments will end up in the final config dictionary, but if two methods define the same key, command line overwrites the configfile statement.

  snakemake --configfile path/to/config.yaml

• in case a module crashes, you manually canceled your jobs or when Snakemake gets stuck trying to "resume.. resubmit.." jobs, then remove the .snakemake/incomplete directory.
• command to generate the directed acyclic graph (DAG) of all jobs with current configuration for visual inspection (most often too large to inspect).

  snakemake --dag --forceall | dot -Tsvg > workflow/dags/all_DAG.svg

• in case of errors during installations, make dure your conda channel priorities are set to "strict"

  conda config --set channel_priority strict

• Finally, if you want to develop your own workflows/modules start with the excellent tutorial from the documentation.