Olamide Isreal
8e3b2170e9
- Remove debug logging and dead PVC/direct-path fallbacks from main.nf - Remove nf-amazon plugin and PVC storage config from nextflow.config (S3 access is handled by boto3 in the script) - Simplify input download and output upload to single boto3 blocks
89 lines
2.6 KiB
Plaintext
89 lines
2.6 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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params.pdb = 's3://omic/eureka/Pocketminer/1HSG.pdb'
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params.outdir = 's3://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:v2'
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input:
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val pdb_path
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output:
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path "results/*", emit: all_results
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path "run.log", emit: log
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script:
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def debug_flag = params.debug ? '--debug' : ''
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def outdir = params.outdir
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"""
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mkdir -p results
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touch run.log
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# Download input PDB from S3/MinIO
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python -c "
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import os, boto3
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from botocore.client import Config
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def get_s3_client():
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return boto3.client('s3',
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endpoint_url=os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000'),
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aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
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aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
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config=Config(signature_version='s3v4'),
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region_name='us-east-1')
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bucket, key = '${pdb_path}'.replace('s3://', '').split('/', 1)
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s3 = get_s3_client()
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s3.download_file(bucket, key, 'input.pdb')
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print(f'Downloaded input ({os.path.getsize(\"input.pdb\")} bytes)')
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" 2>&1 | tee -a run.log
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if [ ! -s input.pdb ]; then
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echo "ERROR: Failed to download PDB file" | tee -a run.log
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exit 1
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fi
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PDB_BASENAME="\$(basename '${pdb_path}' .pdb)"
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# Run PocketMiner prediction
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python /workspace/entrypoint.py \\
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--pdb input.pdb \\
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--output-folder results \\
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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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# Upload results to S3/MinIO
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python -c "
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import os, boto3
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from botocore.client import Config
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def get_s3_client():
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return boto3.client('s3',
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endpoint_url=os.environ.get('AWS_ENDPOINT_URL', 'http://datalake-hl.datalake.svc.cluster.local:9000'),
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aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', ''),
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aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', ''),
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config=Config(signature_version='s3v4'),
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region_name='us-east-1')
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bucket, prefix = '${outdir}'.replace('s3://', '').split('/', 1)
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s3 = get_s3_client()
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for f in os.listdir('results'):
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filepath = os.path.join('results', f)
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if os.path.isfile(filepath):
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key = f'{prefix}/{f}'
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s3.upload_file(filepath, bucket, key)
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print(f'Uploaded {f} -> s3://{bucket}/{key}')
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" 2>&1 | 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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