Recommendations for saving Snakefile and config/cluster files do they don't get overwritten with pulls

HighlanderLab / tree_seq_pipeline

Pipeline to infer tree sequences with different datasets

MIT License

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Recommendations for saving Snakefile and config/cluster files do they don't get overwritten with pulls #48

Closed janaobsteter closed 9 months ago

hannesbecher commented 9 months ago

Config files need not be hard coded into the Snakefile. They can be specified on the commandline with --configfile, see https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html. So, everybody can make their specific config files and leave them untracked.

Happy to add this to the readme.

hannesbecher commented 9 months ago

Also, I think it would be good to have the tsinfer params in a config file rather than in a script file. I just opened #68 about this.

hannesbecher commented 9 months ago

Added recommendations to README.md in PR #69 . Everyone can set up their own config file and specify on the command line via --configfile myFile.yaml. beetest.yaml can be used as a template.