Olamide Isreal
42d4e6cb87
- Add Nextflow pipeline (main.nf) with Harbor container image - Add nextflow.config with k8s/k8s_gpu/standard profiles - Add params.json for TRS/WES parameter discovery - Add Dockerfile, entrypoint.py, meta.yml from original implementation - Update paths to use /omic/eureka/Pocketminer/ convention - Update .gitignore to allow params.json
52 lines
1.8 KiB
JSON
52 lines
1.8 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 cryptic pocket prediction",
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"default": "s3://omic/eureka/Pocketminer/1HSG.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/Pocketminer/1HSG.pdb",
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"s3://omic/eureka/Pocketminer/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 cryptic binding pocket prediction."
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},
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"outdir": {
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"type": "folder",
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"description": "Output directory for PocketMiner prediction results",
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"default": "s3://omic/eureka/Pocketminer/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/Pocketminer/output",
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"s3://omic/eureka/Pocketminer/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 prediction results (numpy arrays, text predictions, and JSON summary) will be stored."
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},
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"debug": {
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"type": "boolean",
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"description": "Save debug features (X, S, mask arrays)",
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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.debug",
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"examples": [
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false,
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true
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],
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"enum": [true, false],
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"validation": {},
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"notes": "Enable to save intermediate feature arrays for debugging purposes."
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}
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}
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}
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