9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
62 lines
2.2 KiB
Plaintext
Executable File
62 lines
2.2 KiB
Plaintext
Executable File
nextflow.enable.dsl=2
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//BIOTRANSFORMER
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params.container_biotransformer = 'biotransformer:latest'
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params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
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params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
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params.project_name = 'test'
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params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
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//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
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params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
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//CONPLEX
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params.container_conplex = 'conplex_dig_pat:latest'
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params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input'
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params.threshold = 0.8 //0.5 //0.7
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params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
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params.protein_network_threshold = 0.95
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//TISSUE DISTRIBUTION
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params.container_tissue = 'tissue:latest'
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//BIOTRANSFORMER
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include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
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include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
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include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
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include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
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include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
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//CONPLEX
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include { CONPLEX } from './main_conplex.nf'
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include { NETWORK_ENRICHMENT } from './main_conplex.nf'
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//TISSUE_DISTRIBUTION
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include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
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workflow {
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//BIOTRANSFORMER
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lig_ch = Channel.fromPath("${params.ligands}/*.csv")
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switch (params.mode) {
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case 'SUPER':
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SUPER_TRANSFORMER(lig_ch)
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break
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case 'HUMAN':
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HUMAN_TRANSFORMER(lig_ch)
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break
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case 'MASS':
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METABOLITES_BY_MASS(lig_ch)
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break
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case 'ORDERED':
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ORDERED_SEQUENCE(lig_ch)
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break
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default:
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println("Invalid mode specified: ${params.mode}")
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}
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GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
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//CONPLEX
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pat_fasta = Channel.fromPath("${params.mutated_protein_fasta}/*.fasta")
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CONPLEX(lig_ch, GET_FINAL_METABOLITES.out, pat_fasta)
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NETWORK_ENRICHMENT(CONPLEX.out.interactions)
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//TISSUE DISTRIBUTION
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TISSUE_DISTRIBUTION(CONPLEX.out.interactions)
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}
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