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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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'use_custom_hlas' not defined in the main script or the params file #70

Closed mantczakaus closed 6 months ago

mantczakaus commented 9 months ago

Hi,

I experienced an issue with running the nextNEOpi with a custom list of HLA alleles. The 'use_custom_hlas' parameter is required here (nextNEOpi.nf) however it's not defined anywhere:

if (! have_HLAHD && run_OptiType) {
    log.warn "WARNING: HLAHD not available - can not predict Class II neoepitopes"
} else if (! have_HLAHD && ! run_OptiType && use_custom_hlas) {
    log.warn "WARNING: HLAHD not available and OptiType disabled - using only user supplied HLA types"
} else if (! have_HLAHD && ! run_OptiType && ! use_custom_hlas) {
    exit 1, "ERROR: HLAHD not available and OptiType disabled - can not predict HLA types"
}

I made a few corrections and it seemed to solve the issue. I can create a pull request if it's correct and would be helpful. nextNEOpi.nf:

have_HLAHD = false
run_OptiType = (params.disable_OptiType) ? false : true
use_custom_hlas = params.use_custom_hlas ? true : false

params.config:

HLA_force_RNA = false  // use only RNAseq for HLA typing
HLA_force_DNA = false  // use only WES/WGS for HLA typing
use_custom_hlas = true

I understand it would be use_custom_hlas = false by default.

Thanks,

Magda