is it necessary to copy this pipeline for each dataset?

[zhangzhen]

the stuff in resources and workflow folder is kept intact, but the stuff in config folder will be changed by users. is there is a better way to run a pipeline without copying it? if a pipeline uses conda envs, the envs are created in <run_dir>/.snakemake/conda/. does copying the pipeline mean these envs are re-created per run?

[sreichl]

Hi @zhangzhen,

• Yes, there is: run the pipeline with user-defined/provided config file see the Snakemake docs here for CLI argument description and here for general explanations.
• Environments, yes that would be the case. That's why we recommend every user to define a global variable where the conda environments should be created (per user) see here my description and here Snakemake's docs.

If this pipeline is useful or interesting to you please consider starring and sharing modules, this helps others to find and benefit from the effort and me to prioritize my efforts! For more modules/pipelines check out MR.PARETO, my effort to augment research by modularizing (biomedical) data science.

I hope this helps! Feel free to close the issue if it's resolved.

Cheers, Stephan