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Digital Trials pipeline configured for WES

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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.
This commit is contained in:
Olamide Isreal
2026-07-27 21:59:52 +01:00
commit 9e75f44f1a
86 changed files with 10142 additions and 0 deletions
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test_bio_metrics_only.nf Normal file
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nextflow.enable.dsl=2
// Default parameters (override via -params-file). Listed here to document every
// parameter this workflow needs. Values copied from a representative job
// (R06-ivan-gabe-bioprops-rerun/J17-bioprops/params.json).
params.container_biotransformer = "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5"
params.container_conplex = "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3"
params.container_tissue = "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.1.0"
params.container_preprocess = "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17"
params.container_mass_screen = "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1"
params.container_chembl = "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0"
params.containerOptions = "--rm"
params.project_name = "bioprops-gabe-run-drug-target"
params.outdir = "/mnt/dreamdock-data/digital_trials/runs/R06-ivan-gabe-bioprops-rerun/J17-bioprops/output"
params.ligands = "/mnt/dreamdock-data/digital_trials/input/gabe-run/input/ligand-drug-target"
params.metabolites = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/screening"
params.conplex_dir = "/mnt/dreamdock-data/digital_trials/input/gabe-run/output/drug-target/conplex"
include { BIO_METRICS } from './main_tissue.nf'
workflow {
lig_ch = Channel.fromPath("${params.ligands}/*.csv")
.map { [it.simpleName, it] }
met_ch = Channel.fromPath("${params.metabolites}/*_out.txt")
.map { f -> [f.simpleName.replaceAll(/_out$/, ''), f] }
drug_ch = Channel.fromPath("${params.conplex_dir}/*_patient_0_drug_scores.tsv")
.map { f -> [f.simpleName.replaceAll(/_patient_0_drug_scores$/, ''), f] }
int_ch = Channel.fromPath("${params.conplex_dir}/*_patient_0_significant_interactions.tsv")
.map { f -> [f.simpleName.replaceAll(/_patient_0_significant_interactions$/, ''), f] }
biometric_ch = lig_ch.join(met_ch).join(drug_ch).join(int_ch)
BIO_METRICS(biometric_ch)
}