Use wildcard on params - bioinformatics

Question

I try to use one tool and I need to use a wildcard present on input.
This is an example:
aDict = {"120":"121" } #tumor : normal
rule all:
input: expand("{case}.mutect2.vcf",case=aDict.keys())
def get_files_somatic(wildcards):
case = wildcards.case
control = aDict[wildcards.case]
return [case + ".sorted.bam", control + ".sorted.bam"]
rule gatk_Mutect2:
input:
get_files_somatic,
output:
"{case}.mutect2.vcf"
params:
genome="ref/hg19.fa",
target= "chr12",
name_tumor='{case}'
log:
"logs/{case}.mutect2.log"
threads: 8
shell:
" gatk-launch Mutect2 -R {params.genome} -I {input[0]} -tumor {params.name_tumor} -I {input[1]} -normal {wildcards.control}"
" -L {params.target} -O {output}"
I Have this error:
'Wildcards' object has no attribute 'control'
So I have a function with case and control. I'm not able to extract code.

Answer 1

The wildcards are derived from the output file/pattern. That is why you only have the wildcard called case. You have to derive the control from that. Try replacing your shell statement with this:
run:
control = aDict[wildcards.case]
shell(
"gatk-launch Mutect2 -R {params.genome} -I {input[0]} "
"-tumor {params.name_tumor} -I {input[1]} -normal {control} "
"-L {input.target2} -O {output}"
)

Answer 2

You could define control in params. Also {input.target2} in shell command would result in error. May be it's supposed to be params.target?
rule gatk_Mutect2:
input:
get_files_somatic,
output:
"{case}.mutect2.vcf"
params:
genome="ref/hg19.fa",
target= "chr12",
name_tumor='{case}',
control = lambda wildcards: aDict[wildcards.case]
shell:
"""
gatk-launch Mutect2 -R {params.genome} -I {input[0]} -tumor {params.name_tumor} \\
-I {input[1]} -normal {params.control} -L {params.target} -O {output}
"""