snakemake wildcards or expand command

Question

I want a rule to perform realignment between normal and tumor. The main problem is I don't know how to manage that problem. Is it the wildcard or the expand the answer to my problem?

This is my list of samples:

conditions:
   pair1:
        tumor: "432"
        normal: "433"

So the rule need to be something like this

rule gatk_RealignerTargetCreator:
    input:
        expand("mapped_reads/merged_samples/{sample}.sorted.dup.reca.bam",sample=config['conditions']['pair1']['tumor']),
        "mapped_reads/merged_samples/{sample}.sorted.dup.reca.bam",sample=config['conditions']['pair1']['normal']),

    output:
        "mapped_reads/merged_samples/{pair1}.realign.intervals"

How can I do this operation for all keys on conditions? (I suppose to have more that one pair)

I have tried this code:

    input:
        lambda wildcards: config["conditions"][wildcards.condition],
        tumor= expand("mapped_reads/merged_samples/{tumor}.sorted.dup.reca.bam",tumor=config['conditions'][wildcards.condition]['tumor']),
        normal = expand("mapped_reads/merged_samples/{normal}.sorted.dup.reca.bam",normal=config['conditions'][wildcards.condition]['normal']),

    output:
        "mapped_reads/merged_samples/{tumor}/{tumor}_{normal}.realign.intervals"

name 'wildcards' is not defined

??

Answer 1

wildcards is not "directly" defined in the input of a rule. You need to use a function of wildcards instead. I'm not sure I understand exactly what you want to do, but you may try something like that.

def condition2tumorsamples(wildcards):
    return expand(
        "mapped_reads/merged_samples/{sample}.sorted.dup.reca.bam",
        sample=config['conditions'][wildcards.condition]['tumor'])

def condition2normalsamples(wildcards):
    return expand(
        "mapped_reads/merged_samples/{sample}.sorted.dup.reca.bam",
        sample=config['conditions'][wildcards.condition]['normal'])

rule gatk_RealignerTargetCreator:
    input:
        tumor = condition2tumorsamples,
        normal = condition2normalsamples,    
    output:
        "mapped_reads/merged_samples/{condition}.realign.intervals"
    # remainder of the rule here...