onenesstwoness support in nf-gos

[jrafailov]

Description of feature

Onenesstwoness has been packaged and shortened to contain its bare necessities for extracting b1/2 scores.

please reconcile pipeline with these changes; see below for the run.R file for proper methodology for calls. note onenesstwoness is dependent on the outputs of homeology/JaBbA_events

SUBJECT TO CHANGE as follows:
hrdetect via call to signaturetools.lib /homeology/onenesstwoness will be collapsed down to own package

options(error={expression({traceback(2); quit('no', 1)})})

library(optparse)
message("Loading input arguments")

if (!exists('opt'))
{
    option_list = list(
        make_option(c("--complex"), type = "character", help = "output of Events.task - path to .rds gGraph object annotated with complex SV event classes"),
        make_option(c("--homeology"), type = "character", help = "output of homeology_hrd.task - path to homeology results"),
        make_option(c("--homeology_stats"), type = "character", help = "output of homeology_hrd.task - path to homeology results, table of each sequence heatmap component for every junction"),
        make_option(c("--hrdetect_results"), type = "character",
                    help = "output of hrdetect_og.task - preferably run with Strelka2 snv and SvAbA indels"),
        make_option(c("--outdir"), type = "character", default = './',
                    help = "output directory")
    )
    message("Found input files")

    parseobj = OptionParser(option_list=option_list)
    opt = parse_args(parseobj)
    message("Parsed input arguments")


    if (
        is.null(opt$complex) 
        || (is.null(opt$homeology)) 
        || is.null(opt$homeology_stats) 
        || is.null(opt$hrdetect_results) 
        )  # was opt$multinomial
        stop(print_help(parseobj))

    print(opt)

    print(.libPaths())
    

    message("Establishing record files")
    ## keep record of run
    writeLines(paste(paste('--', names(opt), ' ', sapply(opt, function(x) paste(x, collapse = ',')), sep = '', collapse = ' '), sep = ''), paste(opt$outdir, 'cmd.args', sep = '/'))
    saveRDS(opt, paste(opt$outdir, 'cmd.args.rds', sep = '/'))
}

message("Loading Packages")
suppressWarnings(expr = {
    suppressPackageStartupMessages(expr = {
            library(gGnome)
            library(onenesstwoness)
        })
})

message("Done Loading Packages")

system(paste('mkdir -p',  opt$outdir))

########## Oneness Twoness #########

predict_hrd(complex = opt$complex,
    homeology = opt$homeology,  
    homeology_stats = opt$homeology_stats, 
    hrdetect_results = opt$hrdetect_results,
    save = TRUE)

quit("no", 0)