Tips and tricks for managing CELLECT snakemake workflows

Configuration

snakemake --configfile <CONFIGFILE.yml>: use specific config file, instead of the default config file (e.g. config-ldsc.yml or config-magma.yml)

Control resources

snakemake --jobs <N>: control the number of parallels jobs.

Check jobs

snakemake --reason --dryrun: Do not execute anything, and display what would be done and print the reason for each executed rule.

snakemake --list-input-changes: List all output files for which the defined input files have changed in the Snakefile

Debugging

snakemake --debug-dag: Print candidate and selected jobs (including their wildcards) while inferring DAG.

snakemake --printshellcmds: Print out the shell commands that will be executed.