Obtain actual --cores [N], --jobs [N], -j [N] value given from command line within the snakefile

Question

How is it possible to access all configuration values and corresponding parameters passed by command line to snakemake, within the snakefile?

For example by running:

snakemake -p --use-conda -j 16 --snakefile ../../Snakefile --configfile pipeline-test.config.yaml

In particular I wish obtain the number of available cores within the snakefile to be able to perform some computation with that value.

score 1 · Answer 1 · answered Feb 26 '19 at 15:03

1

You can use sys.argv within your snakefile to parse the command line parameters.

answered Feb 26 '19 at 15:03

Jan Schreiber

so can I use libraries such as argparse easilly parse command line parameters? – vid1998 Mar 20 '19 at 16:23

1 Answers1