nextflow.enable.dsl=2

// GLOBAL FPSIM2 PARAMS
params.container = 'corto:latest'
params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
params.outdir = '/mnt/OmicNAS/private/old/gabe/corto/outputs'
params.project_name = 'test'

// // INPUTS
params.gene_expression_matrix = '/mnt/OmicNAS/private/old/gabe/corto/inputs/inmat.rda'
params.centroid_list = '/mnt/OmicNAS/private/old/gabe/corto/inputs/centroids.rda'
params.cnv_data = '/mnt/OmicNAS/private/old/gabe/corto/inputs/cnvmat.rda'


include {CORTO} from './main.nf'

workflow {
  gene_expression_matrix = Channel.fromPath(params.gene_expression_matrix)
  centroid_list = Channel.fromPath(params.centroid_list)
  cnv_data = Channel.fromPath(params.cnv_data)
  CORTO(gene_expression_matrix, centroid_list, cnv_data)
}