From 7bfc583bb1631ce525acdbd65353c5b3ecadaba8 Mon Sep 17 00:00:00 2001
From: mhoang22 <98837430+mhoang22@users.noreply.github.com>
Date: Tue, 21 Jan 2025 16:06:30 -0600
Subject: [PATCH] add biotypes and aggregate_inclusion_count_limit in immuno
 wdl input under pvacseq. Note that these 2 inputs are not added to
 subworkflows and tools pvacseq.wdl yet

---
 definitions/immuno.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl
index f31f558..089afdd 100644
--- a/definitions/immuno.wdl
+++ b/definitions/immuno.wdl
@@ -248,11 +248,13 @@ workflow immuno {
     Float? tumor_purity
     Boolean? allele_specific_binding_thresholds
     Int? aggregate_inclusion_binding_threshold
+    Int? aggregate_inclusion_count_limit
     Array[String]? problematic_amino_acids
     Boolean? allele_specific_anchors
     Float? anchor_contribution_threshold
     Int? pvacfuse_read_support
     Float? pvacfuse_expn_val
+    Array[String]? biotypes
 
     # --------- PVACsplice Inputs -----------------------------------------
     # Note: variables similar to PVACseq Inputs or other sections Inputs won't be listed here.