84 lines
2.8 KiB
JSON
Executable File
84 lines
2.8 KiB
JSON
Executable File
{
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"params": {
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"input_dir": {
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"type": "folder",
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"description": "Directory containing FASTA files and optional restraints",
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"default": "s3://omic/eureka/chai1",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.input_dir",
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"examples": [
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"s3://omic/eureka/chai1"
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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 containing FASTA files (with *_complex.fasta suffix) and optional restraints files (with *_restraints.txt suffix)"
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},
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"outdir": {
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"type": "folder",
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"description": "Directory for chai1 prediction results",
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"default": "s3://omic/eureka/chai1/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/chai1/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 prediction results and log files will be stored. Will be created if it doesn't exist."
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},
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"use_msa": {
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"type": "boolean",
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"description": "Enable/disable MSA server usage",
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"default": true,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.use_msa",
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"examples": [
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true,
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false
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],
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"enum": [true, false],
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"validation": {},
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"notes": "Whether to use MSA server for improved predictions"
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},
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"msa_server": {
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"type": "string",
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"description": "MSA server URL",
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"default": "https://api.colabfold.com",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.msa_server",
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"examples": [
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"https://api.colabfold.com"
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],
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"pattern": "^https?://.*",
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"enum": [],
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"validation": {},
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"notes": "URL of the MSA server to use when use_msa is enabled"
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},
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"num_samples": {
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"type": "integer",
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"description": "Number of diffusion samples to generate",
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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.num_samples",
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"examples": [
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5,
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10
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],
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"pattern": "^[1-9]\\d*$",
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"enum": [],
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"validation": {
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"min": 1,
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"max": 50
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},
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"notes": "Number of structure samples to generate using diffusion"
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}
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}
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}
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