Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

main_rna2proteinexpression.nf

@@ -0,0 +1,24 @@
+nextflow.enable.dsl=2
+
+process RNA2PROTEXPRESSION {
+    memory 2.GB
+    accelerator 1
+
+    container "${params.container_rna2protexpression}"
+    label 'gpu_process'
+    //publishDir "${params.outdir_rna2protexpression}", mode: 'copy'
+    // debug true
+    // maxForks 1
+    
+    input:
+     path borzoi_tpm
+
+    output:
+     path "*Protein_Expression_log2.csv", emit: protrin_expression_scores
+     
+    script:
+    """
+    . activate rna2protexpresson
+    python3 /home/omic/rna2protexpression/rna2protexpression.py --borzoi_ouput ${borzoi_tpm}  
+    """
+}