Welcome to Chapulin Discussions!

[DanielRivasMD]

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[Akazhiel]

Hello!

I'm trying to run this tool but I can't find the way of how the config file has to be for the SV module. I try generating a config file with the module provided but it only generates a file that has key = value and this doesn't tell me much about which keys are needed.

Best regards!

[DanielRivasMD]

Hi @Akazhiel,

Thanks for your interest in our tool. Unfortunately, Chapulin is still under development and there are some features that do not properly work yet.

The specific combination of key = value refers to the options that can also be stated at the command line. Below is an example of what I am referring to:

directory = "/home/drivas/private/Phoenix/benchmark_Chapulin/data/Chapulin/chlSab/SAMN06256018/"
output = "outDir/"
mobile_element_library = "REF_chlSab.fa"
mobile_element_alignment = "SAMN06256018_ERV_chlSab_XV.sam"
pair_end_reference_alignment = "SAMN06256018.sorted.RemoveSupplementary.MarkDuplicates.sam"
reference_genome_alignment = "SAMN06256018_R"
threshold_method = "Poisson"
false_discovery_rate = 0.001
expected_tlen = 300
reference = "chlSab2.fa"

I will write more formal documentation about this soon and let you know.

Cheers