Olamide Isreal
8dd0ef8d6a
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- Update container reference to harbor.cluster.omic.ai/omic/propka:latest - Add k8s profile to nextflow.config matching reference tool pattern - Update params.json with s3://omic/eureka/propka/ paths - Add stageInMode 'copy' to process definition - Set params defaults to null for WES compatibility
70 lines
2.4 KiB
JSON
70 lines
2.4 KiB
JSON
{
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"params": {
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"pdb": {
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"type": "file",
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"description": "Path to input PDB file for pKa prediction",
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"default": "s3://omic/eureka/propka/1HPX.pdb",
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"required": true,
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"pipeline_io": "input",
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"var_name": "params.pdb",
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"examples": [
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"s3://omic/eureka/propka/1HPX.pdb",
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"s3://omic/eureka/propka/protein.pdb"
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],
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"pattern": ".*\\.pdb$",
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"enum": [],
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"validation": {},
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"notes": "PDB file containing the protein structure for pKa prediction. Files should be in standard PDB format."
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},
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"outdir": {
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"type": "folder",
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"description": "Output directory for PROPKA prediction results",
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"default": "s3://omic/eureka/propka/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/propka/output",
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"s3://omic/eureka/propka/results"
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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 pKa prediction results will be stored. Will be created if it doesn't exist."
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},
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"ph": {
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"type": "number",
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"description": "pH value for titration calculations",
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"default": 7.0,
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.ph",
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"examples": [
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7.0,
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5.5
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],
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"validation": {
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"min": 0.0,
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"max": 14.0
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},
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"notes": "The pH value used for calculating residue protonation states."
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},
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"options": {
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"type": "string",
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"description": "Additional command-line options for PROPKA",
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"default": "",
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"required": false,
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"pipeline_io": "parameter",
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"var_name": "params.options",
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"examples": [
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"--titrate_only Asp,Glu",
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"--window 1.0"
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],
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"pattern": ".*",
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"enum": [],
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"validation": {},
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"notes": "Additional command-line options to pass to propka3. See propka3 --help for available options."
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}
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}
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}
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