Running locally
This section will focus on local and general options.
Table of contents
Run Snakemake, Run
A typical call to run the data rule may look like this:
snakemake --use-conda --verbose -kprj --res mem_mb=32000 --ri data -n
| Short Option | Long Option | Explanation |
|---|---|---|
--use-conda | Create Conda envs automatically in .snakemake/conda | |
--verbose | Print detailed stack traces and detailed operations | |
-k | --keep-going | If a job fails, continue with independent jobs |
-p | --printshellcmds | |
-r | --reason | Print the reason for rule execution (Missing output, updated input etc.) |
-j | --cores | Number of CPU cores (threads) to use for this run. With no int, it uses all. Default is 1. |
--res | --resources | Key value pair for resources mem_mb: Memory in Megabyte. |
--ri | --rerun-incomplete | If Snakemake marked a file as incomplete after a crash, delete and produce it again |
-n | --dryrun | Just pretend to run the workflow. A similar option is -S (--summary) |
Crashed and burned (Unlocking)
After the workflow was killed (Snakemake didn’t shutdown), the workflow directory will be still locked. If you are sure, that snakemake is no longer running (ps aux | grep snake).
Unlock the working directory:
snakemake data --unlock
Influence rule execution
If you don’t want to delete files marked as temporary in the workflow use the --notemp (--nt) flag. After copying files, modifications date may be altered and Snakemake tries to recreate files. By running Snakemake with the --touch (-t) option, exisitng files will be marked with the current date as current.
If you want to force the recreation of a certain file, use one of the force flags.
| Short Option | Long Option | Explanation |
|---|---|---|
-f | --force | Force execution of the given files or rules |
-F | --forceall | Force execution of the given files or rules and preceding rules |
-R <file> | --forcerules | Force execution of the given file or rule and depending rules |