From 7ec0f399d0c8ffce106b53b6aece974bdd9db690 Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Tue, 6 Aug 2024 10:16:04 +1000
Subject: [PATCH] Allow RNA BAM from samplesheet as input to LILAC

---
 subworkflows/local/lilac_calling/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/lilac_calling/main.nf b/subworkflows/local/lilac_calling/main.nf
index 62e43abe..5ee68fd4 100644
--- a/subworkflows/local/lilac_calling/main.nf
+++ b/subworkflows/local/lilac_calling/main.nf
@@ -193,8 +193,8 @@ workflow LILAC_CALLING {
                 nbai_dna,
                 tbam_dna,
                 tbai_dna,
-                tbam_rna,
-                tbai_rna,
+                Utils.selectCurrentOrExisting(tbam_rna, meta, Constants.INPUT.BAM_RNA_TUMOR),
+                Utils.selectCurrentOrExisting(tbai_rna, meta, Constants.INPUT.BAI_RNA_TUMOR),
                 Utils.selectCurrentOrExisting(purple_dir, meta, Constants.INPUT.PURPLE_DIR),
             ]
         }