Olamide Isreal
f776745722
- Update main.nf: Harbor container image, PVC mount paths, remove containerOptions and stageInMode - Update nextflow.config: Add k8s/k8s_gpu profiles, minimal config for WES injection - Update params.json: Correct paths for eureka PVC - Update Dockerfile.wes: CUDA base image for GPU support
103 lines
3.6 KiB
JSON
103 lines
3.6 KiB
JSON
{
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"params": {
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"protein1_fasta": {
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"type": "file",
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"description": "FASTA file for protein 1",
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"default": "/omic/eureka/bioemu/input/trp_cage.fasta",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.protein1_fasta",
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"examples": [
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"/omic/eureka/bioemu/input/trp_cage.fasta"
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],
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"pattern": ".*\\.fasta$",
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"validation": {},
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"notes": "FASTA file containing the first protein sequence"
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},
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"protein2_fasta": {
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"type": "file",
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"description": "FASTA file for protein 2",
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"default": "/omic/eureka/bioemu/input/villin_headpiece.fasta",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.protein2_fasta",
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"examples": [
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"/omic/eureka/bioemu/input/villin_headpiece.fasta"
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],
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"pattern": ".*\\.fasta$",
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"validation": {},
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"notes": "FASTA file containing the second protein sequence"
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},
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"outdir": {
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"type": "folder",
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"description": "Output directory for results",
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"default": "/omic/eureka/bioemu/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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"/omic/eureka/bioemu/output"
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],
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"pattern": ".*",
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"validation": {},
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"notes": "Directory where prediction results will be stored"
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},
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"complex_name": {
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"type": "string",
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"description": "Name for this protein complex",
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"default": "protein_complex",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.complex_name",
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"examples": [
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"protein_complex"
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]
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},
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"num_samples": {
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"type": "integer",
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"description": "Number of protein structure samples",
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"default": 10,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.num_samples",
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"examples": ["10"],
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"pattern": "^\\d+$",
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"validation": {"min": 1},
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"notes": "More samples provide better coverage of conformational space"
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},
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"temperature": {
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"type": "integer",
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"description": "Temperature (K) for free energy calculations",
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"default": 300,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.temperature",
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"examples": ["300"],
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"pattern": "^\\d+$",
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"validation": {"min": 200, "max": 500},
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"notes": "Temperature in Kelvin"
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},
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"n_clusters": {
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"type": "integer",
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"description": "Number of conformational clusters",
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"default": 5,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.n_clusters",
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"examples": ["5"],
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"pattern": "^\\d+$",
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"validation": {"min": 2}
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},
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"exp_dG": {
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"type": "number",
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"description": "Experimental binding free energy (kcal/mol)",
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"default": -10.0,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.exp_dG",
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"examples": ["-10.0", "-13.1"],
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"notes": "Reference experimental value for comparison"
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}
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}
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}
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