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Update CORTO pipeline with params.json and workflow improvements

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olamide24
2025-03-28 14:45:49 -07:00
parent bf380f2768
commit aaa43a4d54
6 changed files with 127 additions and 92 deletions
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15
test.nf Normal file → Executable file
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@@ -1,22 +1,17 @@
nextflow.enable.dsl=2
// GLOBAL FPSIM2 PARAMS
params.container = 'corto:latest'
params.container_corto = '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'
params.TPM = '/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv'
params.regulon = '/data/olamide/corto/corto_metabolite_prediction/regulon.rda'
//params.TPM_REFERENCE = '/data/olamide/corto/corto_metabolite_prediction/TPM_ENSG_NO_MUTATIONS.csv'
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)
CORTO(params.TPM, params.regulon)// , params.TPM_REFERENCE)
}