重复执行 Snakemake 规则，直到满足某些条件答案

【问题标题】：Execute Snakemake rule repeatedly until certain conditions are met重复执行 Snakemake 规则，直到满足某些条件
【发布时间】：2019-12-30 18:51:09
【问题描述】：

我想将 Snakemake 用于需要重复执行某个步骤直到满足某些条件的流程。无法提前确定该步骤需要多少次。它可以是 1 或 6 或任何其他数字。

我的直觉是，这是 Snakemake 无法做到的，因为有向 非循环 Graph 和所有...

不过，我希望检查点可能会有所帮助，因为它会触发对 DAG 的重新评估，但我只是无法确切了解它是如何工作的。

Snakefile 中的循环是否可能？

谢谢！

在下面的优秀答案中添加一些关于实际发生的事情的评论。希望当我不可避免地重新审视这个问题时，它可以帮助其他人和我自己。

all:  call function all_input to determine rule's input requirements.
all_input:  file "succes.txt" doesn't exist.  do checkpoint keep_trying with i == 1.     
keep_trying:  output "round_1" doesn't exist.  do run section.  random() decides to touch output[0], which is "round_1".

snakemake reevaluates graph after checkpoint is complete

all:  call function all_input to determine rule's input requirements.
all_input:  file "succes.txt" doesn't exist.  do checkpoint keep_trying with i == 2.
keep_trying:   output "round_2" doesn't exist.  do run section.  random() decides to touch output[0], which is "round_2".

snakemake reevaluates graph after checkpoint is complete

all:  call function all_input to determine rule's input requirements.
all_input:  file "succes.txt" doesn't exist.  do checkpoint keep_trying with i == 3.
keep_trying:  output "round_3" doesn't exist.  do run section.  random() decides to touch "succes.txt".

snakemake reevaluates graph after checkpoint is complete

all:  call function all_input to determine rule's input requirements.
all_input:  file "succes.txt" exists.  return "success.txt" to rule all.
all:  input requirement is "success.txt", which is now satisfied.

【问题讨论】：

标签： loops snakemake checkpoint

【解决方案1】：

您是对的，您需要为此设置检查点！这是一个小例子，可以满足您的需求：

import os
from pathlib import Path


tries = 0
def all_input(wildcards):
    global tries
    if not os.path.exists("succes.txt"):
        tries += 1
        checkpoints.keep_trying.get(i=tries)
    else:
        return "succes.txt"


rule all:
    input:
        all_input


checkpoint keep_trying:
    output:
        "round_{i}"
    run:
        import random
        if random.random() > 0.9:
            Path('succes.txt').touch()
        Path(output[0]).touch()

这里我们说rule all 需要从函数all_input 返回的内容作为输入。该函数检查文件succes.txt 是否已经存在。如果不是，它将触发检查点的运行，继续尝试，这可能会生成succes.txt 文件（10% 的机会）。如果succes.txt 确实存在，那么这就是rule all 的输入，并且snakemake 成功退出。

【讨论】：