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!