102 lines
3.7 KiB
JSON
102 lines
3.7 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": "/data/olamide/corto/corto_metabolite_prediction/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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"/data/olamide/corto/corto_metabolite_prediction/20002_1289_female_patient_0_TPM.csv",
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"/path/to/your/sample_TPM.csv"
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],
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"pattern": ".*\\.csv$",
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"enum": [],
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"validation": {},
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"notes": "A CSV file containing TPM values with ENSG IDs as rows and samples as columns"
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},
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"regulon": {
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"type": "file",
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"description": "Path to regulon RDA file",
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"default": "/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.regulon",
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"examples": [
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"/data/olamide/corto/corto_metabolite_prediction/regulon.rda",
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"/path/to/your/custom_regulon.rda"
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],
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"pattern": ".*\\.rda$",
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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": "/mnt/OmicNAS/private/old/gabe/corto/outputs",
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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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"/mnt/OmicNAS/private/old/gabe/corto/outputs",
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"/path/to/custom/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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"project_name": {
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"type": "string",
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"description": "Project name for output directory organization",
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"default": "test",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.project_name",
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"examples": [
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"test",
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"patient_analysis",
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"metabolite_prediction_run1"
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],
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"pattern": "^[A-Za-z0-9_-]+$",
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"enum": [],
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"validation": {},
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"notes": "Name used to create a subdirectory within the output directory"
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},
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"container_corto": {
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"type": "string",
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"description": "Docker container for CORTO",
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"default": "corto:latest",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.container_corto",
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"examples": [
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"corto:latest",
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"yourregistry/corto:v1.0"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Docker container image to use for the CORTO analysis"
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},
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"containerOptions": {
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"type": "string",
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"description": "Docker container options",
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"default": "--gpus all --rm -v /mnt:/mnt",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.containerOptions",
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"examples": [
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"--gpus all --rm -v /mnt:/mnt",
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"--rm -v /custom/path:/mnt"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Options to pass to the Docker container runtime"
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}
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}
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}
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