Snakemake - passing additional parameters to an input function

user_2583346 0
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I am trying to create a Snakemake workflow that takes a TSV table configuration which looks something like this:

sample    path
s1    /path/to/s1_dir
s2    /path/to/s2_dir

For each sample, I provide a directory, from which I use various paths along the workflow.
I would like to be able to get the various inputs with a single input function. I tried this:

import pandas as pd

samples = pd.read_table('samples.tsv').set_index("sample", drop=False)

rule all:
    '...'

def get(wildcards, what):
    sample_dir = samples.loc[wildcards.sample, 'path']
    if what == 1:
        return sample_dir + '/sub/' + 'someInput'
    elif what == 2:
        return sample_dir + '/sub2/' + 'otherInput'

rule rule1:
    input:
        get(what=1)
    ...

rule rule2:
    input:
        get(what=2)
    ...

However, this results in an error message, and according to the documentation, input functions may only take a single parameter (wildcards). I guess one workaround would be having multiple input functions:

def get1(wildcards):
    sample_dir = samples.loc[wildcards.sample, 'path']
    return sample_dir + '/sub/' + 'someInput'

def get2(wildcards):
    sample_dir = samples.loc[wildcards.sample, 'path']
    return sample_dir + '/sub2/' + 'otherInput'

But what if I have 10 different inputs? Any idea how to do that?
Thanks!

snakemake python
1 Answers

That's what I would do. Combine your custom function get with a lambda function:

def get(wildcards, what):
    # Do stuff with wildcards and what
    ...

rule one:
    input:
        lambda wc: get(wc, what= 1)

rule two:
    input:
        lambda wc: get(wc, what= 2)
user_11144530
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