CODEWITHSUNDEEP
snakemake
user9367574
user9367574

Reputation: 91

Snakemake decide which rules to execute during execution

I'm working on a bioinformatics pipeline which must be able to run different rules to produce different outputs based on the contents of an input file:

def foo(file):
 '''
 Function will read the file contents and output a boolean value based on its contents
 '''
# Code to read file here...
return bool

rule check_input:
  input: "input.txt"
  run:
     bool = foo("input.txt")

rule bool_is_True:
  input: "input.txt"
  output: "out1.txt"
  run:
    # Some code to generate out1.txt. This rule is supposed to run only if foo("input.txt") is true

rule bool_is_False:
  input: "input.txt"
  output: "out2.txt"
  run:
    # Some code to generate out2.txt. This rule is supposed to run only if foo("input.txt") is False

How do I write my rules to handle this situation? Also how do I write my first rule all if the output files are unknown before the rule check_input is executed?

Thanks!

Upvotes: 1

Views: 240

Answers (2)

user9367574
user9367574

Reputation: 91

Thanks Eric. I got it work with:

def getTargetsFromInput(file):
    with open(file) as f:
        line = f.readline()
        if line.strip() == "out1":
            return "out1.txt"
        else:
            return "out2.txt"

rule all:
    input: getTargetsFromInput("input.txt")

rule out1:
    input: "input.txt"
    output: "out1.txt"
    run: shell("echo 'out1' > out1.txt")

rule out2:
    input: "input.txt"
    output: "out2.txt"
    run: shell("echo 'out2' > out2.txt")

Upvotes: 1

Eric C.
Eric C.

Reputation: 3368

You're right, snakemake has to know which files to produce before executing the rules. Therefore, I suggest you use a function which reads what you called "the input file" and define the output of the workflow accordingly.

ex:

def getTargetsFromInput():
    targets = list()
    ## read file and add target files to targets
    return targets

rule all:
    input: getTargetsFromInput()

...

You can define the path of the input file with --config argument on the snakemake command line or directly use some sort of structured input file (yaml, json) and use the keyword configfile: in the Snakefile: https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html

Upvotes: 1

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