Olamide Isreal
14091fce87
- Add executor, docker, k8s storage config to k8s profile - Use val input instead of file channel (avoids S3 staging issue) - Pass PDB path as string, copy from PVC mount inside script - Add PVC mount debug logging - Set default params to /omic/eureka paths
62 lines
1.9 KiB
Plaintext
62 lines
1.9 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// Pipeline parameters
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params.pdb = '/omic/eureka/Pocketminer/1HSG.pdb'
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params.outdir = '/omic/eureka/Pocketminer/output'
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params.model_path = '/workspace/gvp/models/pocketminer'
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params.debug = false
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process POCKETMINER {
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container 'harbor.cluster.omic.ai/omic/pocketminer:latest'
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publishDir params.outdir, mode: 'copy'
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input:
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val pdb_path
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output:
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path "*-preds.npy", emit: predictions_npy
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path "*-predictions.txt", emit: predictions_txt
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path "*-summary.json", emit: summary
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path "*_X.npy", optional: true, emit: features_debug
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path "*_S.npy", optional: true, emit: sequence_debug
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path "*_mask.npy", optional: true, emit: mask_debug
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path "run.log", emit: log
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script:
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def pdb_basename = file(pdb_path).baseName
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def debug_flag = params.debug ? '--debug' : ''
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"""
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touch run.log
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echo "=== Debugging PVC mount ===" | tee -a run.log
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echo "Input path: ${pdb_path}" | tee -a run.log
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ls -la /omic/eureka/ 2>&1 | head -20 | tee -a run.log
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ls -la /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
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echo "=== End Debug ===" | tee -a run.log
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if [ ! -f "${pdb_path}" ]; then
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echo "ERROR: PDB file not found at ${pdb_path}" | tee -a run.log
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echo "Available files in /omic/eureka/Pocketminer/:" | tee -a run.log
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ls /omic/eureka/Pocketminer/ 2>&1 | tee -a run.log || true
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exit 1
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fi
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cp "${pdb_path}" input.pdb
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python /workspace/entrypoint.py \\
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--pdb input.pdb \\
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--output-folder . \\
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--output-name ${pdb_basename} \\
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--model-path ${params.model_path} \\
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${debug_flag} 2>&1 | tee -a run.log
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echo "Pipeline completed successfully" | tee -a run.log
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"""
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}
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workflow {
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POCKETMINER(params.pdb)
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}
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