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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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{
"container_biotransformer": "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5",
"container_conplex": "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3",
"container_tissue": "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.2",
"container_preprocess": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17",
"container_mass_screen": "harbor.cluster.omic.ai/omic/metabolite-screen:adaptive-1.1.1",
"container_chembl": "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0",
"containerOptions": "--rm",
"project_name": "test2",
"mode": "HUMAN",
"keep_enst": false,
"threshold": 0.65,
"protein_network_threshold": 0.65,
"outdir": "/mnt/dreamdock-data/digital_trials/output/test2",
"ligands": "/mnt/dreamdock-data/digital_trials/input/input_knowen_target",
"mutated_protein_fasta": "/mnt/dreamdock-data/digital_trials/input/blank",
"protein_zarr": "/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr",
"chembl_db": "/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db"
}

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params/input_to_run.json Normal file
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{
"container_biotransformer": "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5",
"container_conplex": "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3",
"container_tissue": "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.2",
"container_preprocess": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17",
"container_mass_screen": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:89fe2221ff6c1e67d20294944f97418f2665d95b9fb873eba9e1fcf3dc6d1ea7",
"container_chembl": "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0",
"containerOptions": "--rm",
"mode": "HUMAN",
"keep_enst": false,
"threshold": 0.65,
"protein_network_threshold": 0.65,
"project_name": "input_to_run",
"outdir": "/mnt/dreamdock-data/digital_trials/output",
"ligands": "/mnt/dreamdock-data/digital_trials/input/input_to_run",
"mutated_protein_fasta": "/mnt/dreamdock-data/digital_trials/input/blank",
"protein_zarr": "/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr",
"chembl_db": "/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db"
}