How to make Snakemake wildcard work for empty string?

Question

I expected Snakemake to allow wildcards to be empty strings, alas, this isn't the case.

How can I make a wildcard accept an empty string?

Answer 1

Wildcards by default only match the regex .+ meaning everything but empty strings. This is unfortunately not documented beyond a Google group conversation.

To make a wildcard accept empty strings, simply add a custom wildcard constraint wildcard_constraints: foo=".*", either within the scope of a rule or globally:

# Option 1
wildcard_constraints:
    foo=".*"

rule a:
    input: in{foo}.txt
    output: out{foo}.txt
    wildcard_constraints: foo=".*"  # Option 2
    shell: "cp {input} {output}"