Is it possible to enable/disable certain Snakemake rules using command line flags

Question

Is it possible to have the snakemake file and/or the rules files configured to execute certain rules only in certain cases using command line switches.

To elaborate, lets say I have these rules in my rules folder:

• rule 1
• rule 2a
• rule 2b
• rule 2c
• rule 3

Is it possible to configure/execute the workflow in this way:

• call snakemake --user_option 2a will cause rule 1, rule 2a, rule 3 to be invoked
• call snakemake --user_option 2b will cause rule 1, rule 2b, rule 3 to be invoked
• and so on

Thanks in advance.

Answer 1

You could pass the user_option as a configuration key at the command line and then have an if-else that decides what intermediate rule to use. E.g.

snakemake --config option='2a'

The dummy Snakefile:

rule all:
    input:
        'output.txt',

rule one:
    output:
        'foo.txt'

if config['option'] == '2a':
    rule two_a:
        input:
            'foo.txt',
        output:
            'bar.txt',
elif config['option'] == '2b':
    rule two_b:
        input:
            'foo.txt',
        output:
            'bar.txt',
else:
    sys.exit() ## handle this case

rule three:
    input:
        'bar.txt',
    output:
        'output.txt',