Snakemake，“ lambda通配符，尝试，线程”麻烦

Question

I was using snakemake to implement a new tool in a pipeline and i had some trouble with those lines:

resources:
    # Samtools sort requires by default 768M per threads
    # Here, be set the maximum amount of memory are 1.5Go per threads
    mem_mb = (
        lambda wildcards, attempt, threads: min(
        attempt * 250 + threads * 768,
        1536 * threads)
    )

the error is :

TypeError: <lambda>() missing 1 required positional argument: 'threads'
Wildcards:
sample=test_GATK
genome=fakefile

To make those lines i used the documentation on this page : snakemake documentation

To fix this issue i use this code instead:

resources:
    # Samtools sort requires by default 768M per threads
    # Here, be set the maximum amount of memory are 1.5Go per threads
    mem_mb = (
        lambda wildcards, attempt: min(
        attempt * 250 + config["threads"] * 768,
        1536 * config["threads"])
    )

I don't know why the previous one is not working, can you help me figure it out ?

Thanks for the help :)

Answer 1

My reading of the docs is that callable requires 4 parameters and you supply 3 out of order.

Maybe make a lambda with 4 args? If it where mot an init file, I would also say - make a function instead of a lambda and then 3 keyword args can fit.