Snakemake executor plugin: cannon

Warning

This plugin is not maintained and reviewed by the official Snakemake organization.

Warning

No documentation found in repository https://github.com/harvardinformatics/snakemake-executor-plugin-cannon. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instructions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-cannon

Usage

In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:

snakemake --executor cannon ...

with ... being any additional arguments you want to use.

Settings

The executor plugin has the following settings (which can be passed via command line, the workflow or environment variables, if provided in the respective columns):

Settings

CLI argument	Description	Default	Choices	Required	Type
--cannon-logdir VALUE	Per default the SLURM log directory is relative to the working directory.This flag allows to set an alternative directory.	None		✗
--cannon-keep-successful-logs VALUE	Per default SLURM log files will be deleted upon sucessful completion of a job. Whenever a SLURM job fails, its log file will be preserved. This flag allows to keep all SLURM log files, even those of successful jobs.	False		✗
--cannon-delete-logfiles-older-than VALUE	Per default SLURM log files in the SLURM log directory of a workflow will be deleted after 10 days. For this, best leave the default log directory unaltered. Setting this flag allows to change this behaviour. If set to <=0, no old files will be deleted.	10		✗
--cannon-init-seconds-before-status-checks VALUE	Defines the time in seconds before the first status check is performed after job submission.	40		✗
--cannon-status-attempts VALUE	Defines the number of attempts to query the status of all active jobs. If the status query fails, the next attempt will be performed after the next status check interval.The default is 5 status attempts before giving up. The maximum time between status checks is 180 seconds.	5		✗
--cannon-requeue VALUE	Allow requeuing preempted of failed jobs, if no cluster default. Results in sbatch … –requeue … This flag has no effect, if not set.	False		✗
--cannon-no-account VALUE	Do not use any account for submission. This flag has no effect, if not set.	False		✗
--cannon-resources VALUE	Print information about the Cannon cluster and exit.	False		✗