如何编写没有输出的 Snakemake 规则？
我的 Snakefile 有一个 print_to_screen 规则没有明确的输出文件。下面是一个简化的例子：
rule all:
placeholder_output # What should I put here?
rule create_file:
output:
"file.txt"
shell:
"echo Hello World! > {output}"
rule print_to_screen: # This rule has no output
input:
"file.txt"
shell:
"cat {input}"
如何编写print_to_screen规则，使其触发其他规则，意思是：
- 它可以作为其他规则中的输入，所以运行
snakemake {placeholder_output}也会触发之前的规则create_file？ - 它可以包含在
rule all中，因此运行snakemake会触发所有规则？
My Snakefile has a print_to_screen rule with no explicit output file. The following is a simplified example:
rule all:
placeholder_output # What should I put here?
rule create_file:
output:
"file.txt"
shell:
"echo Hello World! > {output}"
rule print_to_screen: # This rule has no output
input:
"file.txt"
shell:
"cat {input}"
How can I write the print_to_screen rule so that it triggers other rules, meaning that:
- it can be used as an input in other rules, so running
snakemake {placeholder_output}also triggers the previous rulecreate_file? - it can be included in
rule all, so runningsnakemaketriggers all rules?
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规则的
output部分是可选的，但您需要将其设为第一个规则（将其定义为 Snakefile 中的第一个规则）才能生效：如果您需要一些灵活性（例如您有多个类似的规则）你应该使用 标志。
The
outputsection of the rule is optional, but you need to make it the first rule (define it the first in your Snakefile) to take any effect:If you need some flexibility (for example you have several rules like that) you should use flags.