英文:
How to make Snakemake wildcard work for empty string?
问题
我期望Snakemake允许通配符为空字符串，然而，事实并非如此。
如何使通配符接受空字符串？
英文:
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?
答案1
得分: 4
通配符默认只匹配正则表达式.+，意味着匹配一切除了空字符串。不幸的是，除了Google小组讨论之外，这一点未记录。
要使通配符匹配空字符串，只需在规则范围内或全局添加自定义通配符约束wildcard_constraints: foo=".*"：
# 选项 1
wildcard_constraints:
foo=".*"
rule a:
input: in{foo}.txt
output: out{foo}.txt
wildcard_constraints: foo=".*" # 选项 2
shell: "cp {input} {output}"
英文:
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}"
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