如何为Snakemake自动生成的输出目标分配可读标签？

我有一个输出高度冗余的Snakemake规则（已简化）：

rule redundant:
    output:
        a_x = "prefix_a_x.ext"
        b_x = "prefix_b_x.ext"
        a_y = "prefix_a_y.ext"
        b_y = "prefix_b_y.ext"
    run:
        process_1(output.a_x)
        process_2(output.a_y)
        process_3(output.b_x)
        process_4(output.b_y)

使用列表推导式可减少冗余，但会降低可读性（需通过索引访问输出，不够直观）：

rule less_readable:
    output:
        [f"prefix_{a}_{b}.ext"
         for a in ["a", "b"]
         for b in ["x", "y"]]
    run:
        process_1(output[0])
        process_2(output[1])
        process_3(output[2])
        process_4(output[3])

注：不想使用expand("prefix_{a}_{b}.ext", a=["a", "b"], b=["x", "y"])，因为输出顺序很重要，担心未来Snakemake版本会改变其顺序。

尝试用字典推导式兼顾冗余减少与可读性，却触发报错：

rule more_readable:
    output:
        {f"{a}_{b}": f"prefix_{a}_{b}.ext"
         for a in ["a", "b"]
         for b in ["x", "y"]}
    run:
        process_1(output.a_x)
        process_2(output.a_y)
        process_3(output.b_x)
        process_4(output.b_y)

执行命令snakemake -j 1 prefix_a_x.ext时的报错信息：

Building DAG of jobs...
MissingRuleException:
No rule to produce prefix_a_x.ext (if you use input functions make sure that they don't raise unexpected exceptions).

解决方法 #

在Snakemake 7.x版本中，不能直接在output段使用字典推导式生成带标签的输出，但可以通过**字典解包（**操作符）**实现需求，既减少冗余，又保留标签可读性和顺序可控性：

方式1：提前定义输出字典 #

# 预先定义带标签的输出字典，确保顺序符合预期
outputs_dict = {
    f"{a}_{b}": f"prefix_{a}_{b}.ext"
    for a in ["a", "b"]
    for b in ["x", "y"]
}

rule optimized_readable:
    output:
        **outputs_dict  # 解包字典作为带标签的输出项
    run:
        process_1(output.a_x)
        process_2(output.a_y)
        process_3(output.b_x)
        process_4(output.b_y)

方式2：直接在output段内解包推导式 #

rule optimized_readable:
    output:
        **{
            f"{a}_{b}": f"prefix_{a}_{b}.ext"
            for a in ["a", "b"]
            for b in ["x", "y"]
        }
    run:
        process_1(output.a_x)
        process_2(output.a_y)
        process_3(output.b_x)
        process_4(output.b_y)

以上两种写法既能通过推导式消除冗余代码，又能像原始规则一样通过标签（如output.a_x）访问输出文件，同时Snakemake能正确识别每个输出文件对应的规则，避免MissingRuleException报错。

内容的提问来源于stack exchange，提问作者abukaj