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.

.gitignore

@@ -0,0 +1,24 @@
+/work
+.nextflow
+.nextflow.*
+sample/
+*.swp
+*.pid
+*.log
+
+# Large files (baked into Docker images or staged to S3)
+ensemble_reference.fasta
+go_df_work.csv
+MANE_transcipts_reference.fasta
+reference.fasta
+MANE.GRCh38.v1.3.update.tsv
+go_term_protein_expression_model.pth
+CIBERSORTx-fractionshires/
+TPM_NO_MUTATIONS.csv
+name_transcipt_map.csv
+LM22_sourceGEP_ensg.txt
+regulon.rda
+impute-me_wget_ukbb_variants.sh
+ncbiRefSeq_subset.pickle
+prot_subset.pickle
+app_filter/Cosmic_GenomeScreensMutant_v103_GRCh38.vcf.gz