From a430a1e21801e54ff66aa1b353b6fb94e4b649b7 Mon Sep 17 00:00:00 2001
From: Darryl Nousome <dnousome@gmail.com>
Date: Tue, 19 Nov 2024 14:47:12 -0500
Subject: [PATCH] fix: use sample sheet name in gridss output for continuity

---
 modules/local/structural_variant.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/local/structural_variant.nf b/modules/local/structural_variant.nf
index fc61e6e..5e44b7a 100644
--- a/modules/local/structural_variant.nf
+++ b/modules/local/structural_variant.nf
@@ -129,6 +129,7 @@ process gridss_somatic {
     """
     gridss --jar /opt2/gridss/gridss-2.13.2-gridss-jar-with-dependencies.jar \
     -r $BWAGENOME \
+    -l ${normalname},${tumorname} \
     -o ${tumorname}_vs_${normalname}.vcf.gz -b $BLACKLIST \
     --picardoptions VALIDATION_STRINGENCY=LENIENT \
     --jvmheap 90g \
@@ -190,6 +191,7 @@ process gridss_tonly {
     """
     gridss --jar /opt2/gridss/gridss-2.13.2-gridss-jar-with-dependencies.jar \
     -r $BWAGENOME \
+    -l ${tumorname} \
     -o ${tumorname}.vcf.gz -b $BLACKLIST \
     --picardoptions VALIDATION_STRINGENCY=LENIENT \
     ${tumor} -t $task.cpus