Olamide Isreal
88627edc25
- Add main.nf as WES entry point with PVC-based paths - Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc) - Update params.json defaults to /omic/eureka/digital-patients/ paths - Remove stageInMode 'copy' from corto and vcf2prot for k8s compat - Add reassemble.nf for one-time chunk reassembly on PVC
46 lines
1.1 KiB
Plaintext
46 lines
1.1 KiB
Plaintext
nextflow.enable.dsl=2
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process CORTO {
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memory 1.GB
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container "${params.container_corto}"
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containerOptions "${params.containerOptions}"
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publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
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// debug true
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// maxForks 1
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input:
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path TPM
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path regulon
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// path TPM_ref
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// Define output channels
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output:
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path "*_metabolome.csv", emit: csv_metabol
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script:
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"""
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#!/usr/bin/Rscript
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library(corto)
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library(data.table)
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TPM <- as.matrix(fread("$TPM"),rownames=1)
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#TPM_ref <- as.matrix(fread("TPM_ref"),rownames=1) #dollar sign is missing
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#try normalization; dont use
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#TPM <- scale(TPM)
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#TPM_log2 = log2(TPM + 1)
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load("$regulon")
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predicted<-mra(TPM, regulon=regulon)
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#use this if we want to compare patients and reference TPM, data formet output is not csv -> work on data saving if needed
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#predicted<-mra(TPM, path TPM_ref, regulon=regulon)
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name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])], split = "_TPM.csv")[[1]][1]
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name = paste(name, "_metabolome.csv", sep="")
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write.csv(predicted, name)
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"""
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}
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