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
43 lines
1.4 KiB
YAML
43 lines
1.4 KiB
YAML
params:
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- outdir:
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type: file
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description: path where output files will be deposited
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required: true
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- model_path:
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type: file
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description: path to pre-trained PocketMiner model checkpoint
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default: /workspace/gvp/models/pocketminer
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required: false
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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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input:
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- pdb:
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type: file
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description: PDB file path for protein structure
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- dynamics_optional:
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type: file
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description: optional MD trajectory or ensemble of conformers for enhanced cryptic pocket detection
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required: false
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output:
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- predictions_npy:
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type: file
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description: NumPy binary file containing per-residue cryptic pocket scores
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- predictions_txt:
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type: file
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description: human-readable text file with per-residue cryptic pocket scores (4 decimal places)
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- summary:
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type: file
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description: JSON file containing overall cryptic pocket score, high/medium confidence residue counts, pocket clusters, and metadata
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- features_debug:
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type: file
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description: (optional) protein features array for debugging
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- sequence_debug:
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type: file
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description: (optional) sequence data array for debugging
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- mask_debug:
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type: file
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description: (optional) masking array for debugging
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