snakemake how to encode pair analisys - bioinformatics

Question

I want to use gatk recalibration using pair sample ( tumor and normal). I need to parse the data using pandas. That is what I wroted.
expand("mapped_reads/merged_samples/{sample[1][tumor]}/{sample[1][tumor]}_{sample[1][normal]}.bam", sample=read_table(config["conditions"], ",").iterrows())
this is the condition file:
432,433
434,435
I wrote this rule:
rule gatk_RealignerTargetCreator:
input:
"mapped_reads/merged_samples/{tumor}.sorted.dup.reca.bam",
"mapped_reads/merged_samples/{normal}.sorted.dup.reca.bam",
output:
"mapped_reads/merged_samples/{tumor}/{tumor}_{normal}.realign.intervals"
params:
genome=config['reference']['genome_fasta'],
mills= config['mills'],
ph1_indels= config['know_phy'],
log:
"mapped_reads/merged_samples/logs/{tumor}_{normal}.realign_info.log"
threads: 8
shell:
"gatk -T RealignerTargetCreator -R {params.genome} {params.custom} "
"-nt {threads} "
"-I {wildcard.tumor} -I {wildcard.normal} -known {params.ph1_indels} "
"-o {output} >& {log}"
I have this error:
InputFunctionException in line 17 of /home/maurizio/Desktop/TEST_exome/rules/samfiles.rules:
KeyError: '432/432_433'
Wildcards:
sample=432/432_433
this is the samfiles.rules:
rule samtools_merge_bam:
"""
Merge bam files for multiple units into one for the given sample.
If the sample has only one unit, files will be copied.
"""
input:
lambda wildcards: expand("mapped_reads/bam/{unit}_sorted.bam",unit=config["samples"][wildcards.sample])
output:
"mapped_reads/merged_samples/{sample}.bam"
benchmark:
"benchmarks/samtools/merge/{sample}.txt"
run:
if len(input) > 1:
shell("/illumina/software/PROG2/samtools-1.3.1/samtools merge {output} {input}")
else:
shell("cp {input} {output} && touch -h {output}")

Answer 1

I can only guess because you don't show all relevant rule, but I would say the error occurs because the rule samtools_merge_bam also applies to some later bam file where you have the pattern {tumor}/{tumor}_{normal}...
As a solution, you have to resolve this ambiguity (see the snakemake tutorial). For example, you can constrain the wildcard of samtools_merge_bam to not contain any slashes.
wildcard_constraints:
sample="[^/]+"
You can put the constraint either globally or inside your samtools_merge_bam rule.