Question

此处给出的print()示例 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#local-rules 显示了如何显式列出应在主机节点上执行的规则。

是否可以在运行时添加规则，以工作流程的参数为条件？

例如看起来像下面的东西？

localrules:

我尝试了以下操作，并带有警告，指示my_local_rules = ['rule1', 'rule_2'] if condition: my_local_rules.append('rule3') localrules: my_local_rules指令没有执行我想要的操作。

localrules

具体地说，它失败并显示以下错误：

local_rules_list = ['all']

if True:
   local_rules_list.append('test')

localrules: local_rules_list

rule all:
    input:
        # The first rule should define the default target files
        # Subsequent target rules can be specified below. They should start with all_*.
        "results/test.out"


rule test:
    input:
        "workflow/Snakefile"
    output:
        "results/test.out"
    shell:
        "cp {input} {output}"

我的特定用例是同时具有本地模式和Cell Ranger的软件cluster mode。

在本地模式下，localrules directive specifies rules that are not present in the Snakefile: local_rules_list命令作为作业提交到计算节点上。在群集模式下，cellranger命令应在头节点上运行，因为cellranger本身负责将作业提交给计算节点。

我希望我的工作流程让用户选择运行Cell Ranger的模式（例如cellranger或local），因此，如果sge工作流程将添加以下规则：将mode: sge运行到cellranger。这可能吗，还是只能在Snakefile中对本地规则进行硬编码？

最好，凯文

Answer 1

谢谢

@ Maarten-vd-Sande的post linked中建议的“ hack”对我来说很好。

在这个玩具示例中，我对建议的技巧进行了如下修改。即：

规则all是在localrules指令中明确设置的
将规则test1添加到使用hack的本地规则集中，表明使用了虚拟条件
规则test2是一个否定控件，任何时候都不会添加到本地规则列表中


# The main entry point of your workflow.
# After configuring, running snakemake -n in a clone of this repository should successfully execute a dry-run of the workflow.


report: "report/workflow.rst"

# Allow users to fix the underlying OS via singularity.
singularity: "docker://continuumio/miniconda3"

localrules: all

rule all:
    input:
        # The first rule should define the default target files
        # Subsequent target rules can be specified below. They should start with all_*.
        "results/test1.out",
        "results/test2.out"


rule test1:
    input:
        "workflow/Snakefile"
    output:
        "results/test1.out"
    shell:
        "cp {input} {output}"

      
rule test2:
    input:
        "workflow/Snakefile"
    output:
        "results/test2.out"
    shell:
        "cp {input} {output}"


include: "rules/common.smk"
include: "rules/other.smk"


# Conditionally add rules to the directive 'localrules'
_localrules = list(workflow._localrules) # get the local rules so far

if True: # set condition here
    _localrules.append('test1') # add rules as required

workflow._localrules = set(_localrules) # set the updated local rules

谢谢！

是否可以将规则动态添加到“ localrules：”？

1 个答案: