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.

main_tissue.nf

@@ -0,0 +1,57 @@
+nextflow.enable.dsl=2
+
+
+process TISSUE_DISTRIBUTION {
+    memory { params.tissue_initial_memory.toInteger().GB + (task.attempt - 1) * params.tissue_growth_memory.toInteger().GB }
+
+    container "${params.container_tissue}"
+    // containerOptions "${params.containerOptions}"
+    publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
+    // // Temporarily disabled debug prints
+    // debug true
+
+    errorStrategy { task.attempt <= params.tissue_max_retries.toInteger() ? 'retry' : params.tissue_fail_action }
+    maxRetries params.tissue_max_retries.toInteger()
+
+    input:
+     path interaction
+
+    output:
+     path "*tissue_distribution.tsv", emit: tissue_dist
+
+    script:
+    """
+    # . activate tissue
+    python /home/omic/drug_tissue_distribution.py --file_name ${interaction}
+    """
+}
+
+process BIO_METRICS {
+    memory { params.bio_initial_memory.toInteger().GB + (task.attempt - 1) * params.bio_growth_memory.toInteger().GB }
+
+    container "${params.container_tissue}"
+    // containerOptions "${params.containerOptions}"
+    publishDir "${params.outdir}/${params.project_name}/4_tissue_distribution", mode: 'copy'
+    // debug true
+
+    errorStrategy { task.attempt <= params.bio_max_retries.toInteger() ? 'retry' : params.bio_fail_action }
+    maxRetries params.bio_max_retries.toInteger()
+
+    input:
+      tuple (
+        val(id),
+        path( target),
+        path( metabolites),
+        path( conplex_drug),
+        path( conplex_all_interactions),
+     )
+
+    output:
+     path "*_biological_properties.tsv", emit: bio_prop
+
+    script:
+    """
+    # . activate tissue
+    python /home/omic/digital_patient_extract_metrics.py --metabolites ${metabolites} --conplex_all_interactions ${conplex_all_interactions} --conplex_drug ${conplex_drug} --target ${target}
+    """
+}