Snakemake pipeline with Gatk GermlineCNVCaller in Case mode

Question

[slowbromain]

Hi everyone,

I am trying to set up a Snakemake pipeline for germline CNV calling with Gatk in CASE mode since I have a background ready to use . My background is fragmented in 20 shards (something like ../cohort-twenty/name_1of20-model), and the GermlineCNVCaller tool has to be runned a number of times equal to the number of shards, creating 20 different "calls" output (like sample-vs-cohort_0001of20-calls). Those output calls, along with the model shards, are going to be the input for the following rule PostProcessGermlineCNVCalls, which I can handle. Therefore I need to run the GermlineCNVCaller rule 20 times. Does anybody have some solution to how run the same rule a fixed number of times? Thank you very much!

Answer 1

[Pierre Lindenbaum]

see https://gitlab.univ-nantes.fr/benjamin.co/sv-exome/-/blob/master/Snakefile_exome ?

[slowbromain]

thank you Pierre