Is it possible to dynamically add rules to 'localrules:'? [duplicate] - snakemake

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snakemake list rules to execute in cluster and local
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Closed 2 years ago.
The example of localrules: given here
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#local-rules
shows how to explicitly list rules that should be executed on the host node.
Is there a way to add rules at runtime, conditioning them on parameters of the workflow?
e.g. something that would look like the following?
my_local_rules = ['rule1', 'rule_2']
if condition:
my_local_rules.append('rule3')
localrules: my_local_rules
I've tried the following, which runs with a warning, indicating that the localrules directive is not doing what I'd like.
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}"
Specifically, it fails with the following error:
localrules directive specifies rules that are not present in the Snakefile:
local_rules_list
My specific use case is the software Cell Ranger which has both a local mode and a cluster mode.
In local mode, the cellranger command is submitted as a job on a compute node.
In cluster mode, the cellranger command should run on the head node, as cellranger itself handles the job submission to the compute nodes.
I would like my workflow to let users choose which mode to run Cell Ranger (e.g. local or sge) and as a result, if mode: sge the workflow would add the rule that runs cellranger to localrules: ....
Is that possible, or can local rules only be hard coded in the Snakefile?
Best,
Kevin

Answer 1

Thanks
The 'hack' suggested in the post linked in #Maarten-vd-Sande's comment works fine for me.
I have adapted the suggested hack as follows, in this toy example.
Namely:
rule all is explicitly set in the localrules directive
rule test1 is added to the set of local rules using the hack, demonstrating the use of a dummy condition, as I illustrated in my question
rule test2 is here as a negative control that is not added to list of local rules at any point
# 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
Thanks!