Digital Trials pipeline configured for WES

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.

test.nf.save

@@ -0,0 +1,49 @@
+nextflow.enable.dsl=2
+
+//BIOTRANSFORMER
+params.container_biotransformer = 'biotransformer:latest'
+params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
+params.outdir = '/mnt/OmicNAS/private/old/gabe/digital_trials'
+params.project_name = 'test'
+params.ligands = '/Workspace/next/registry/pipelines/digital_trials/input'
+
+//IMPOTRANT!!! use HUMAN. Only one that returns what is expected. metabolism to the last step. It's only one properly set up
+params.mode = 'HUMAN' // Options: SUPER, HUMAN, MASS, ORDERED # only HUMAN is fully implemented
+
+//CONPLEX
+params.container_conplex= 'conplex_dig_pat'
+params.mutated_protein_fasta = '/Workspace/next/registry/pipelines/digital_trials/input/*.fasta'
+params.threshold = 0.2 //0.75
+params.screening_batch_size =100000 //100k is ideal to optimize performance with virtual screening
+
+//BIOTRANSFORMER
+include { SUPER_TRANSFORMER } from './main_biotransformer.nf'
+include { HUMAN_TRANSFORMER } from './main_biotransformer.nf'
+include { METABOLITES_BY_MASS } from './main_biotransformer.nf'
+include { ORDERED_SEQUENCE } from './main_biotransformer.nf'
+include { GET_FINAL_METABOLITES } from './main_biotransformer.nf'
+//CONPLEX
+include { CONPLEX } from './main_conplex.nf'
+
+workflow {
+    //BIOTRANSFORMER
+    lig_ch = Channel.fromPath("${params.ligands}/*.csv")
+    switch (params.mode) {
+        case 'SUPER':
+            SUPER_TRANSFORMER(lig_ch)
+            break
+        case 'HUMAN':
+            HUMAN_TRANSFORMER(lig_ch)
+            break
+        case 'MASS':
+            METABOLITES_BY_MASS(lig_ch)
+            break
+        case 'ORDERED':
+            ORDERED_SEQUENCE(lig_ch)
+            break
+        default:
+            println("Invalid mode specified: ${params.mode}")
+    }
+    GET_FINAL_METABOLITES(HUMAN_TRANSFORMER.out)
+    //CONPLEX
+}