From 457d35146653cde15984413b5e23f5bed79ae6d4 Mon Sep 17 00:00:00 2001
From: Tanubrata Dey <tdey@nygenome.org>
Date: Mon, 27 Nov 2023 09:55:36 -0500
Subject: [PATCH] Bugfix: Fixes GRIDSS slurm killing

---
 modules/local/gridss/gridss/main.nf | 6 +++---
 workflows/nfjabba.nf                | 5 +++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/modules/local/gridss/gridss/main.nf b/modules/local/gridss/gridss/main.nf
index 1d5a6df..1152c27 100644
--- a/modules/local/gridss/gridss/main.nf
+++ b/modules/local/gridss/gridss/main.nf
@@ -39,15 +39,15 @@ process GRIDSS_GRIDSS {
     """
     ${bwa}
 
-    gridss \\
+        gridss \\
         --output ${prefix}.vcf.gz \\
         --reference ${fasta} \\
         --threads ${task.cpus} \\
         $assembly_bam \\
         $blacklist \\
         --picardoptions VALIDATION_STRINGENCY=LENIENT \\
-        --jvmheap ${task.memory.toGiga() - 1}g \\
-        --otherjvmheap ${task.memory.toGiga() - 1}g \\
+        --jvmheap 31g \\
+        --otherjvmheap 31g \\
         ${normalbam} \\
         ${tumorbam}
 
diff --git a/workflows/nfjabba.nf b/workflows/nfjabba.nf
index ce9262a..ce88b40 100644
--- a/workflows/nfjabba.nf
+++ b/workflows/nfjabba.nf
@@ -1243,8 +1243,9 @@ workflow NFJABBA {
 
                 // A conditional check to see if for some reason ASCAT failed and ploidy is empty
                 ploidy = ploidy.ifEmpty { 
-                    [ input_sample[0][0], ploidy_jab ]
-                }
+                    input_sample.map { tuple -> [tuple[0], ploidy_jab] } 
+                    }
+                
                 ploidy_jabba = ploidy // If ASCAT is used and it is not empty, then use the value from ASCAT
 
             } else {