From 142fb0bbc1fea73c8d02f86211fc82113759ac68 Mon Sep 17 00:00:00 2001
From: riasc <richard.schaefer@zoho.com>
Date: Thu, 14 Mar 2024 13:03:04 -0500
Subject: [PATCH] fixed typo that caused snvs to be called with indels

---
 workflow/rules/common.smk | 8 ++++----
 workflow/rules/indel.smk  | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index 5384198..39d189f 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -641,20 +641,20 @@ def get_shortindels(wildcards):
   return indels
 
 def get_snvs(wildcards):
-  indels=[]
+  snvs=[]
   if config['indel']['mode'] in ['RNA','BOTH']:
-    indels += expand("results/{sample}/{seqtype}/indel/mutect2/{group}_somatic.snvs.vcf.gz",
+    snvs += expand("results/{sample}/{seqtype}/indel/mutect2/{group}_somatic.snvs.vcf.gz",
       sample=config['data']['name'], 
       seqtype='rnaseq',
       group=list(config['data']['rnaseq'].keys()))
   
   if config['indel']['mode'] in ['DNA','BOTH']:
-    indels += expand("results/{sample}/{seqtype}/indel/mutect2/{group}_somatic.snvs.vcf.gz",
+    snvs += expand("results/{sample}/{seqtype}/indel/mutect2/{group}_somatic.snvs.vcf.gz",
       sample=config['data']['name'], 
       seqtype='dnaseq',
       group=list(config['data']['dnaseq'].keys()))
 
-  return indels
+  return snvs
 
 
 ########### EXITRON CALLING ##########
diff --git a/workflow/rules/indel.smk b/workflow/rules/indel.smk
index b553501..7f20fb4 100644
--- a/workflow/rules/indel.smk
+++ b/workflow/rules/indel.smk
@@ -406,7 +406,7 @@ rule sort_somatic_SNVs_m2:
 
 rule combine_somatic_SNVs_m2:
   input:
-    get_shortindels
+    get_snvs
   output:
     "results/{sample}/variants/somatic.snvs.vcf.gz"
   message: