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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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64
params.json
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@@ -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"
}
}
}