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
45 lines
1.1 KiB
Plaintext
45 lines
1.1 KiB
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl=2
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// 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 definition
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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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stageInMode 'copy'
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input:
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path pdb_file
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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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script:
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def pdb_basename = pdb_file.baseName
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def debug_flag = params.debug ? '--debug' : ''
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"""
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python /workspace/entrypoint.py \\
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--pdb ${pdb_file} \\
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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}
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"""
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}
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// Workflow
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workflow {
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POCKETMINER(Channel.of(file(params.pdb)))
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}
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