Configuration of Snakemake#

To set up a profile for custom Snakemake command line arguments, create a new profile (config.yaml) in $HOME/.config/snakemake/standard/:

cores: 40 # Maximum number of cores to use
latency-wait: 10
use-conda: True
rerun-incomplete: True
printshellcmds: True
show-failed-logs: True
use-apptainer: True # Set to False on MacOS or if you do not want to use Apptainer

It is recommend to set both use-conda and use-apptainer to True, as this will ensure that the workflow runs in a reproducible environment.

When running GPSW on a cluster it is recommended to also add the following settings:

executor: slurm # for SLURM cluster
jobs: 100 # Maximum number of jobs to run in parallel
apptainer-args: "--bind '/rds/gps/'" # if analysis in not in /home/$USER
local-cores: 2 # Limit core usage for local rules
default-resources:
      slurm_partition: <PARTITION>
      slurm_account: <ACCOUNT>

Note

If you are running the analysis using Apptainer outside of your home directory, you need to bind the directory where the analysis is located. For example, if your analysis is in /rds/gps/, you can use apptainer-args: “–bind ‘/rds/gps/’”.

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