Olamide Isreal
4bbc9822af
- 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
50 lines
1.7 KiB
JSON
50 lines
1.7 KiB
JSON
{
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"params": {
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"TPM": {
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"type": "file",
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"description": "Path to TPM (Transcripts Per Million) CSV file",
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"default": "s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.TPM",
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"examples": [
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"s3://omic/eureka/corto/20002_1289_female_patient_0_TPM.csv"
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],
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"pattern": ".*\\.csv$",
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"enum": [],
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"validation": {},
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"notes": "A CSV file containing TPM values with ENSG IDs as rows and samples as columns"
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},
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"regulon": {
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"type": "file",
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"description": "Path to regulon RDA file",
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"default": "s3://omic/eureka/corto/regulon.rda",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.regulon",
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"examples": [
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"s3://omic/eureka/corto/regulon.rda"
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],
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"pattern": ".*\\.rda$",
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"enum": [],
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"validation": {},
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"notes": "An R data file containing regulon information for the CORTO analysis"
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},
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"outdir": {
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"type": "folder",
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"description": "Directory for CORTO analysis results",
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"default": "s3://omic/eureka/corto/output",
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"required": true,
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"pipeline_io": "output",
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"var_name": "params.outdir",
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"examples": [
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"s3://omic/eureka/corto/output"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Directory where metabolome prediction results will be stored"
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}
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}
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}
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