Olamide Isreal
8887cbe592
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- Update container image to harbor.cluster.omic.ai/omic/immunebuilder:latest - Update input/output paths to S3 (s3://omic/eureka/immunebuilder/) - Remove local mount containerOptions (not needed in k8s) - Update homepage to Gitea repo URL - Clean history to remove large model weight blobs
84 lines
3.3 KiB
JSON
84 lines
3.3 KiB
JSON
{
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"params": {
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"fasta": {
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"type": "file",
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"description": "Path to input FASTA file(s) containing immune protein sequences",
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"default": "s3://omic/eureka/immunebuilder/antibody_test.fasta",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.fasta",
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"examples": [
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"s3://omic/eureka/immunebuilder/antibody.fasta",
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"s3://omic/eureka/immunebuilder/*.fasta"
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],
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"pattern": ".*\\.(fasta|fa|faa)$",
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"enum": [],
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"validation": {},
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"notes": "FASTA format requirements vary by mode. Antibody: >H (heavy chain) and >L (light chain). Nanobody: >H (heavy chain only). TCR: >A (alpha chain) and >B (beta chain)."
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},
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"outdir": {
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"type": "folder",
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"description": "Directory for ImmuneBuilder prediction output files",
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"default": "s3://omic/eureka/immunebuilder/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/immunebuilder/output",
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"s3://omic/eureka/immunebuilder/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 predicted PDB structures and log files will be stored. Will be created if it doesn't exist."
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},
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"mode": {
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"type": "string",
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"description": "Prediction mode specifying the type of immune protein",
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"default": "antibody",
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"required": true,
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"pipeline_io": "parameter",
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"var_name": "params.mode",
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"examples": [
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"antibody",
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"nanobody",
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"tcr"
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],
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"pattern": "^(antibody|nanobody|tcr)$",
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"enum": ["antibody", "nanobody", "tcr"],
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"validation": {},
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"notes": "Determines which predictor to use: 'antibody' for ABodyBuilder2, 'nanobody' for NanoBodyBuilder2, 'tcr' for TCRBuilder2."
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},
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"verbose": {
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"type": "boolean",
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"description": "Enable verbose output during prediction",
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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.verbose",
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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": "When enabled, provides detailed progress information during structure prediction."
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},
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"original_weights": {
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"type": "boolean",
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"description": "Use original TCRBuilder2 weights instead of TCRBuilder2+ weights",
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"default": false,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.original_weights",
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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": "Only applicable when mode is 'tcr'. By default, TCRBuilder2+ weights are used. Set to true to use the original TCRBuilder2 weights."
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}
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}
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}
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