corto up and running!

test.nf

@@ -0,0 +1,22 @@
+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)
+}