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.

test_no_mutations.nf

@@ -0,0 +1,14 @@
+nextflow.enable.dsl=2
+
+params.container_borzoi = 'borzoi:latest'
+params.containerOptions = '--gpus all --rm -v /mnt:/mnt'
+params.outdir = '/mnt/OmicNAS/private/old/gabe/borzoi/outputs'
+params.project_name = 'test'
+
+params.mane = '/Workspace/next/registry/pipelines/digital_patient/MANE.GRCh38.v1.3.update.tsv'
+
+include {PREDICT_EXPRESSION_NO_MUTATIONS} from './main_no_mutations.nf'
+
+workflow {
+    PREDICT_EXPRESSION_NO_MUTATIONS(params.mane)
+}