From 67d4607f4aa6aafd5cd9a268e1b68a3180abea27 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 27 Aug 2024 15:35:08 +0200
Subject: [PATCH] update cytosure conditional

---
 workflows/raredisease.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index 10ef83b1..8dbfae62 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -785,7 +785,7 @@ workflow RAREDISEASE {
     Generate CGH files from sequencing data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-    if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") ) {
+    if ( !params.skip_vcf2cytosure && params.analysis_type.equals("wgs") && !params.skip_sv_calling) {
         GENERATE_CYTOSURE_FILES (
             ch_sv_annotate.vcf_ann,
             ch_sv_annotate.tbi,