Snakemake抱怨找不到在運行指令中應該創建的文件

Question

考慮以下簡單的蛇文件，這是嘗試在run指令中寫入文件的嘗試：

rule all:
    input:
        "test.txt"

rule make_test:
    output:
        filename = "test.txt"
    run:
        with open(output.filename) as f:
            f.write("test")

運行它會導致以下結果：

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   all
    1   make_test
    2
rule make_test:
    output: test.txt
Error in job make_test while creating output file test.txt.
RuleException:
FileNotFoundError in line 10 of /tmp/Snakefile:
[Errno 2] No such file or directory: 'test.txt'
  File "/tmp/Snakefile", line 10, in __rule_make_test
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

我對此FileNotFoundError感到驚訝。 很顯然，我沒有找到正確的方法來告訴snakemake，這是我想要的規則文件make_test創建。

我還嘗試了輸出語法的以下修改：

rule all:
    input:
        "test.txt"

rule make_test:
    output:
        "test.txt"
    run:
        with open(output[0]) as f:
            f.write("test")

錯誤是一樣的。

發生了什么？

Answer 1

我發現了該錯誤的原因：我只是忘記了以寫入模式打開文件：

全部規則：輸入：“ test.txt”

以下作品：

rule make_test:
    output:
        "test.txt"
    run:
        with open(output[0], "w") as f:
            f.write("test")