snakemake if else statement within rule input - snakemake

Question

With snakemake, I would like to have a different input (including a wildcard) within a rule according to a boolean
I've tried :
rule quantify:
input:
if trimmed_fastq:
forward = path_trimmed_fastq + "/{sample}_R1_val_1.fq.gz",
rev = path_trimmed_fastq + "/{sample}_R2_val_2.fq.gz"
else:
forward = fastq_path + "/{sample}_R1.fastq.gz",
rev = fastq_path + "/{sample}_R2.fastq.gz"
But it gives me an "invalid syntax" error, I think it doesn't like if else statement in input, anyone has an idea how to fix this?
I know I could have two different "quantify" and "quantify_trimmed" rules with if else statement around them, but I'm wondering if there is a more elegant solution.
Thank you for your help

Answer 1

Indeed, you cannot have an if..else statement inside an input. Instead, a function can be used to achieve what you want:
def getInputFilesForQuantify(wildcards):
files = dict()
if(trimmed_fastq):
files["forward"] = os.path.join(path_trimmed_fastq,wildcards.sample,"_R1_val_1.fq.gz")
files["rev"] = os.path.join(path_trimmed_fastq,wildcards.sample,"_R2_val_2.fq.gz")
else:
files["forward"] = os.path.join(fastq_path,wildcards.sample,"_R1.fastq.gz")
files["rev"] = os.path.join(fastq_path,wildcards.sample,"_R2.fastq.gz")
return files
rule quantify:
input: unpack(getInputFilesForQuantify)
output: ....
Note:
wildcards are passed to the parameters of the function.
unpack is here used because you're returning a dictionnary if naming of your inputs are needed. Otherwise, a simple list of files is returned.