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.
94 lines
3.6 KiB
Plaintext
94 lines
3.6 KiB
Plaintext
nextflow.enable.dsl=2
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// Digital-trials pipeline WITHOUT biotransformer.
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// Metabolites are supplied externally (e.g. the consolidated final-metabolites
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// dir from prior gabe runs). Otherwise identical to test.nf.
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//
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// New required param vs test.nf:
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// params.metabolites - dir of `<stem>_out.txt` files matching ligand `<stem>.csv`
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// Dropped (no biotransformer/chembl):
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// container_biotransformer, container_chembl, bt_* knobs, chembl_db, mode
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params.container_conplex = 'harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3'
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params.container_tissue = 'harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.6'
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params.container_preprocess = 'harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17'
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params.container_mass_screen = 'harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1'
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params.containerOptions = '--rm'
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params.project_name = 'test_no_bt'
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//CONPLEX
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params.keep_enst = 'false'
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params.conplex_initial_memory = 5
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params.conplex_growth_memory = 15
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params.conplex_max_retries = 1
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params.conplex_fail_action = 'ignore'
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params.threshold = 0.65
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params.protein_network_threshold = 0.65
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// NETWORK_ENRICHMENT (string-db)
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params.string_max_forks = 5
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params.string_max_retries = 1
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params.string_fail_action = 'ignore'
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params.string_initial_memory = 1
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params.string_growth_memory = 2
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// TISSUE_DISTRIBUTION + BIO_METRICS
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params.tissue_initial_memory = 5
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params.tissue_growth_memory = 5
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params.tissue_max_retries = 2
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params.tissue_fail_action = 'ignore'
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params.bio_initial_memory = 5
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params.bio_growth_memory = 5
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params.bio_max_retries = 2
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params.bio_fail_action = 'ignore'
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// ========================================= FILEPATHS ===================================================
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params.outdir = '/mnt/omic-next-apis/wes/digital_trials/'
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params.ligands = '/mnt/dreamdock-data/digital_trials/input/test_multitaget'
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params.metabolites = '/mnt/dreamdock-data/digital_trials/input/test_metabolites'
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params.mutated_protein_fasta = '/mnt/dreamdock-data/digital_trials/input/blank'
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params.protein_zarr = '/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr'
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// =====================================================================================================================================
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include { CONPLEX as CONPLEX_ALL } from './main_conplex.nf'
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include { PREPROCESS_PROTEIN } from './main_conplex.nf'
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include { NETWORK_ENRICHMENT } from './main_conplex.nf'
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include { TISSUE_DISTRIBUTION } from './main_tissue.nf'
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include { BIO_METRICS } from './main_tissue.nf'
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workflow {
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lig_ch = Channel.fromPath("${params.ligands}/*.csv")
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metabolite_ch = Channel.fromPath("${params.metabolites}/*_out.txt")
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protein_fasta = Channel
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.fromPath("${params.mutated_protein_fasta}/*.fasta")
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.collect()
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protein_zarr = PREPROCESS_PROTEIN(protein_fasta).collect().map { it[0] }
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pre_protein_zarr = Channel.fromPath(params.protein_zarr)
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merged_zarr = protein_zarr.concat(pre_protein_zarr).collect()
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lig_with_id = lig_ch.map { csv ->
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[csv.simpleName, csv]
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}
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metabolite_with_id = metabolite_ch.map { txt ->
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def name = txt.simpleName.replaceAll(/_out$/, '')
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[name, txt]
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}
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matched_ch = lig_with_id.join(metabolite_with_id)
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CONPLEX_ALL(matched_ch, merged_zarr)
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conplex_interactions_ch = CONPLEX_ALL.out.map { id, drug, interactions -> interactions }
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NETWORK_ENRICHMENT(conplex_interactions_ch)
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TISSUE_DISTRIBUTION(conplex_interactions_ch)
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biometric_ch = matched_ch.join(CONPLEX_ALL.out)
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BIO_METRICS(biometric_ch)
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}
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