CODEWITHSUNDEEP
snakemake
rioualen
rioualen

Reputation: 968

How to get the working directory path?

I'm wondering how to manage paths in my Snakefiles. Say I have this configuration:

current_dir
current_dir/snakefiles
current_dir/configfiles

and I execute my workflows this way:

current_dir$ snakemake -s snakefiles/my_snakefile --configfile configfiles/my_config.yml

I know I can get the path to my Snakefile using the global variable workflow.snakefile, but I would like to get also:

How to achieve this? Are there other global variables in Snakemake, that I'm not aware of?

Thank you

Upvotes: 2

Views: 3761

Answers (1)

Johannes Köster
Johannes Köster

Reputation: 1947

The working directory is set via Python. You can get it with os.getcwd(). Also please note that there is a canonical way to organize Snakemake workflows: http://snakemake.readthedocs.io/en/latest/project_info/faq.html#what-is-the-recommended-way-to-distribute-a-snakemake-workflow.

While you can of course use something else, following this scheme helps others to understand your workflow. There might of course be cases where this does not fit.

Upvotes: 6

Related Questions