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snakemake 8 config file

ManabuIshiiManabuIshii

From snakemake 8 , --cluster option changed.

I think this is document for configuration.
Configuration | Snakemake 8.18.2 documentation https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html

I introduce my case.

setup these 2files
/home/manabu/.config/snakemake/sge
├── cluster.yaml
└── config.yaml

0 directories, 2 files

cluster.yaml looks like this.
I think this file define some variables.

$ cat ~/.config/snakemake/sge/cluster.yaml 
__default__:
  queue: all.q
  threads: 4

config.yaml looks like this
I think this file define actual command
formally --cluster option's value

$ cat ~/.config/snakemake/sge/config.yaml 
executor: cluster-generic
cluster-generic-submit-cmd: "qsub -l nc={threads} -p -50 -r yes -q {queue}"
default-resources: []