CODEWITHSUNDEEP
pipelinesnakemakebamgatk
Franz
Franz

Reputation: 35

How to deal with paired tumor-normal samples in Snakemake?

I am converting a bash pipeline to process paired whole-exome sequenced tumor-normal samples into a SnakeMake workflow.

Paired samples are listed in my config file, as follows:

sample_list:
  - sample: 1
    tumor: AO1_04_RN_1_T_4_S4
    control: AO2_07_C007558T1Wa_S37
  - sample: 2
    tumor: AO2_01_C007589T1FTa_S2
    control: AO2_07_C007589T1Wa_S34
  - sample: 3
    tumor: AO9_09_FM_1_T_7_S13 
    control: AO2_07_C007558T1Wa_S37

I am now stuck in getting a rule to call variants with Mutect2 to process the tumor samples from sample X specifically with its control sample (e.g. for sample 1: -I tumor_of_sample_1 -I control_of_sample_1).

What I keep getting (even using zip) is a command built like this: -I tumor_of_sample_1 tumor_of_sample_2 tumor_of_sample_3 -I control_of_sample_1 control_of_sample_2 control_of_sample_3, which inevitably fails.

I would be very grateful for some help...thanks!

Upvotes: 0

Views: 56

Answers (1)

kEks
kEks

Reputation: 588

I think what you need is a simple lambda function to grab the correct config entry for a given wildcard.I changed your config file a bit, which makes the lambda function a bit simpler, otherwise it should be trivial to adjust the function accordingly (I think, have not tested it)

sample_list:
    sample1:
      tumor: sample1_tumor.gz
      control: sample1_control.gz
    sample2:
      tumor: sample2_tumor.gz
      control: sample2_control.gz
    sample3:
      tumor: sample2_tumor.gz
      control: sample2_control.gz

And the conresponding snakefile:

configfile: "config.yml"

rule all:
    input:
        expand("out/{ID}.procesed",ID=["sample1","sample2","sample3"])

rule test:
    input:
        tumor=lambda wc: "input/"+config["sample_list"][wc.ID]["tumor"],
        control=lambda wc: "input/"+config["sample_list"][wc.ID]["control"]
    output:
        "out/{ID}.procesed"
    shell:
        "echo {input.tumor} {input.control} {output}"

Upvotes: 2

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