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Configure corto for WES k8s execution

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- Update main.nf: hardcode Harbor container image, add workflow block,
  use PVC mount path defaults, remove stageInMode copy and legacy params
- Update nextflow.config: add k8s profile with container, add process
  resource limits, update manifest to point to Gitea
- Update params.json: use s3:// prefixed paths for WES, remove
  container_corto, containerOptions, and project_name params
This commit is contained in:
Olamide Isreal
2026-03-25 15:12:40 +01:00
parent aaa43a4d54
commit 4bbc9822af
3 changed files with 50 additions and 85 deletions
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28
main.nf
View File

@@ -1,19 +1,21 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// Parameters
params.TPM = '/omic/eureka/corto/20002_1289_female_patient_0_TPM.csv'
params.regulon = '/omic/eureka/corto/regulon.rda'
params.outdir = '/omic/eureka/corto/output'
process CORTO {
container "${params.container_corto}"
containerOptions "${params.containerOptions}"
publishDir "${params.outdir}/${params.project_name}", mode: 'copy'
container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
publishDir params.outdir, mode: 'copy'
debug true
// maxForks 1
stageInMode 'copy'
input:
path TPM
path regulon
// path TPM_ref
// Define output channels
output:
path "*_metabolome.csv", emit: csv_metabol
@@ -24,21 +26,17 @@ process CORTO {
library(data.table)
TPM <- as.matrix(fread("$TPM"),rownames=1)
#TPM_ref <- as.matrix(fread("TPM_ref"),rownames=1) #dollar sign is missing
#try normalization; dont use
#TPM <- scale(TPM)
#TPM_log2 = log2(TPM + 1)
load("$regulon")
predicted<-mra(TPM, regulon=regulon)
#use this if we want to compare patients and reference TPM, data formet output is not csv -> work on data saving if needed
#predicted<-mra(TPM, path TPM_ref, regulon=regulon)
name = strsplit(strsplit("$TPM", split = "/")[[1]][length(strsplit("$TPM", split = "/")[[1]])], split = "_TPM.csv")[[1]][1]
name = paste(name, "_metabolome.csv", sep="")
write.csv(predicted, name)
"""
}
workflow {
CORTO(Channel.of(file(params.TPM)), Channel.of(file(params.regulon)))
}

41
nextflow.config
View File

@@ -1,15 +1,34 @@
manifest {
name = 'corto'
author = 'omic'
recurseSubmodules = true
homePage = 'https://gitlab.com/omic/next/registry/tools/corto'
description = ''
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.3'
defaultBranch = 'master'
name = 'corto'
author = 'omic'
homePage = 'https://trs-gitea.cluster.omic.ai/omic/corto'
description = 'CORTO - Correlation Tool for gene regulatory network analysis'
mainScript = 'main.nf'
version = '1.0.0'
defaultBranch = 'master'
}
docker {
enabled = true
temp = 'auto'
params {
TPM = null
regulon = null
outdir = null
}
profiles {
standard {
docker {
enabled = true
temp = 'auto'
}
}
k8s {
process {
container = 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
}
}
}
process {
cpus = 1
memory = '4 GB'
}

64
params.json
View File

@@ -3,13 +3,12 @@
"TPM": {
"type": "file",
"description": "Path to TPM (Transcripts Per Million) CSV file",
"default": "/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
"default": "s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv",
"required": true,
"pipeline_io": "input",
"var_name": "params.TPM",
"examples": [
"/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
"/path/to/your/sample_TPM.csv"
"s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv"
],
"pattern": ".*\\.csv$",
"enum": [],
@@ -19,13 +18,12 @@
"regulon": {
"type": "file",
"description": "Path to regulon RDA file",
"default": "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
"default": "s3://omic/eureka/corto/regulon.rda",
"required": true,
"pipeline_io": "input",
"var_name": "params.regulon",
"examples": [
"/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
"/path/to/your/custom_regulon.rda"
"s3://omic/eureka/corto/regulon.rda"
],
"pattern": ".*\\.rda$",
"enum": [],
@@ -35,67 +33,17 @@
"outdir": {
"type": "folder",
"description": "Directory for CORTO analysis results",
"default": "/mnt/OmicNAS/private/old/gabe/corto/outputs",
"default": "s3://omic/eureka/corto/output",
"required": true,
"pipeline_io": "output",
"var_name": "params.outdir",
"examples": [
"/mnt/OmicNAS/private/old/gabe/corto/outputs",
"/path/to/custom/output"
"s3://omic/eureka/corto/output"
],
"pattern": ".*",
"enum": [],
"validation": {},
"notes": "Directory where metabolome prediction results will be stored"
},
"project_name": {
"type": "string",
"description": "Project name for output directory organization",
"default": "test",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.project_name",
"examples": [
"test",
"patient_analysis",
"metabolite_prediction_run1"
],
"pattern": "^[A-Za-z0-9_-]+$",
"enum": [],
"validation": {},
"notes": "Name used to create a subdirectory within the output directory"
},
"container_corto": {
"type": "string",
"description": "Docker container for CORTO",
"default": "corto:latest",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.container_corto",
"examples": [
"corto:latest",
"yourregistry/corto:v1.0"
],
"pattern": ".*",
"enum": [],
"validation": {},
"notes": "Docker container image to use for the CORTO analysis"
},
"containerOptions": {
"type": "string",
"description": "Docker container options",
"default": "--gpus all --rm -v /mnt:/mnt",
"required": false,
"pipeline_io": "parameter",
"var_name": "params.containerOptions",
"examples": [
"--gpus all --rm -v /mnt:/mnt",
"--rm -v /custom/path:/mnt"
],
"pattern": ".*",
"enum": [],
"validation": {},
"notes": "Options to pass to the Docker container runtime"
}
}
}