Access workdir defined on command line from within Snakefile

Question

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 --directory?

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?

Answer 1

You could query Python for the working directory within the Snakefile, since evidently Snakemake changes the actual working directory of the process to the one specified by --directory. For example, using a stub Snakefile with just these two lines:

import os
print("Current working directory: " + os.getcwd())

And on the command line:

$ snakemake --directory working-directory
Creating specified working directory working-directory.
Current working directory: /home/jesse/dev/snakemake-wd/working-directory
Building DAG of jobs...
Nothing to be done.
Complete log: /home/jesse/dev/snakemake-wd/working-directory/.snakemake/log/2019-08-02T142009.349338.snakemake.log