Configure bioemu for WES deployment
- 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
This commit is contained in:
112
params.json
112
params.json
@@ -1,78 +1,81 @@
|
||||
{
|
||||
"params": {
|
||||
"fasta_list": {
|
||||
"type": "file[]",
|
||||
"description": "FASTA files containing protein sequences",
|
||||
"default": [],
|
||||
"protein1_fasta": {
|
||||
"type": "file",
|
||||
"description": "FASTA file for protein 1",
|
||||
"default": "/omic/eureka/bioemu/input/trp_cage.fasta",
|
||||
"required": true,
|
||||
"pipeline_io": "input",
|
||||
"var_name": "params.fasta_list",
|
||||
"var_name": "params.protein1_fasta",
|
||||
"examples": [
|
||||
["/omic/olamide/examples/prot1.fasta", "/omic/olamide/examples/prot2.fasta"]
|
||||
"/omic/eureka/bioemu/input/trp_cage.fasta"
|
||||
],
|
||||
"pattern": ".*\\.fasta$",
|
||||
"validation": {},
|
||||
"notes": "Select one or more FASTA files with protein sequences"
|
||||
"notes": "FASTA file containing the first protein sequence"
|
||||
},
|
||||
"protein2_fasta": {
|
||||
"type": "file",
|
||||
"description": "FASTA file for protein 2",
|
||||
"default": "/omic/eureka/bioemu/input/villin_headpiece.fasta",
|
||||
"required": true,
|
||||
"pipeline_io": "input",
|
||||
"var_name": "params.protein2_fasta",
|
||||
"examples": [
|
||||
"/omic/eureka/bioemu/input/villin_headpiece.fasta"
|
||||
],
|
||||
"pattern": ".*\\.fasta$",
|
||||
"validation": {},
|
||||
"notes": "FASTA file containing the second protein sequence"
|
||||
},
|
||||
"outdir": {
|
||||
"type": "folder",
|
||||
"description": "Output Directory",
|
||||
"default": "/omic/olamide/output",
|
||||
"description": "Output directory for results",
|
||||
"default": "/omic/eureka/bioemu/output",
|
||||
"required": true,
|
||||
"pipeline_io": "output",
|
||||
"var_name": "params.outdir",
|
||||
"examples": [
|
||||
"/omic/olamide/output"
|
||||
"/omic/eureka/bioemu/output"
|
||||
],
|
||||
"pattern": ".*",
|
||||
"validation": {},
|
||||
"notes": "Select where to save your analysis results"
|
||||
"notes": "Directory where prediction results will be stored"
|
||||
},
|
||||
"complex_name": {
|
||||
"type": "string",
|
||||
"description": "Name for this protein complex",
|
||||
"default": "protein_complex",
|
||||
"required": false,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.complex_name",
|
||||
"examples": [
|
||||
"protein_complex"
|
||||
]
|
||||
},
|
||||
"num_samples": {
|
||||
"type": "integer",
|
||||
"description": "Number of protein structure samples",
|
||||
"default": 10,
|
||||
"required": true,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.num_samples",
|
||||
"examples": [
|
||||
"10"
|
||||
],
|
||||
"pattern": "^\\d+$",
|
||||
"validation": {
|
||||
"min": 1
|
||||
},
|
||||
"notes": "More samples provide better coverage of conformational space"
|
||||
},
|
||||
"batch_size_100": {
|
||||
"type": "integer",
|
||||
"description": "Batch size parameter",
|
||||
"default": 10,
|
||||
"required": false,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.batch_size_100",
|
||||
"hidden": true,
|
||||
"examples": [
|
||||
"10"
|
||||
],
|
||||
"pattern": "^\\d+$"
|
||||
"var_name": "params.num_samples",
|
||||
"examples": ["10"],
|
||||
"pattern": "^\\d+$",
|
||||
"validation": {"min": 1},
|
||||
"notes": "More samples provide better coverage of conformational space"
|
||||
},
|
||||
"temperature": {
|
||||
"type": "integer",
|
||||
"description": "Temperature (K) for free energy",
|
||||
"description": "Temperature (K) for free energy calculations",
|
||||
"default": 300,
|
||||
"required": false,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.temperature",
|
||||
"examples": [
|
||||
"300"
|
||||
],
|
||||
"examples": ["300"],
|
||||
"pattern": "^\\d+$",
|
||||
"validation": {
|
||||
"min": 200,
|
||||
"max": 500
|
||||
},
|
||||
"notes": "Temperature in Kelvin for free energy calculations"
|
||||
"validation": {"min": 200, "max": 500},
|
||||
"notes": "Temperature in Kelvin"
|
||||
},
|
||||
"n_clusters": {
|
||||
"type": "integer",
|
||||
@@ -81,26 +84,19 @@
|
||||
"required": false,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.n_clusters",
|
||||
"examples": [
|
||||
"5"
|
||||
],
|
||||
"examples": ["5"],
|
||||
"pattern": "^\\d+$",
|
||||
"validation": {
|
||||
"min": 2
|
||||
},
|
||||
"notes": "Number of clusters for free energy analysis"
|
||||
"validation": {"min": 2}
|
||||
},
|
||||
"cache_dir": {
|
||||
"type": "folder",
|
||||
"description": "Embeddings cache directory",
|
||||
"default": "/tmp/bioemu_cache",
|
||||
"exp_dG": {
|
||||
"type": "number",
|
||||
"description": "Experimental binding free energy (kcal/mol)",
|
||||
"default": -10.0,
|
||||
"required": false,
|
||||
"pipeline_io": "parameter",
|
||||
"var_name": "params.cache_dir",
|
||||
"hidden": true,
|
||||
"examples": [
|
||||
"/tmp/bioemu_cache"
|
||||
]
|
||||
"var_name": "params.exp_dG",
|
||||
"examples": ["-10.0", "-13.1"],
|
||||
"notes": "Reference experimental value for comparison"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user