Snakemake provides access to a
workflow object within a Snakefile. This allows one to, for example, have dynamic programmatic access to the directory containing the Snakefile (via the
workflow.basedir attribute). Is there a similar way to access the working directory that is specified on the command line using
Through a bit of exploration I was able to figure out that the
workflow object has a
workdir() method, but it appears this is used internally by Snakemake for registering working directories, not for access.
UPDATE: It looks like the working directory is stored internally as the
_workdir attribute of the
workflow object. However, this attribute is unset (default value
None) when I'm creating static/global objects in the Snakefile. Is it impossible to access the working directory prior to building the workflow DAG?