From 4653c99a224f4d02e3e33180f0fabe03bfda25b2 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Mon, 4 Mar 2024 15:42:58 +0100
Subject: [PATCH] Set temp directory for mutect2

---
 modules/local/mutect2.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/local/mutect2.nf b/modules/local/mutect2.nf
index c5964a9..87ec0f3 100644
--- a/modules/local/mutect2.nf
+++ b/modules/local/mutect2.nf
@@ -20,6 +20,7 @@ process MUTECT2 {
         -callable-depth 6 \
         --native-pair-hmm-threads ${task.cpus} \
         --max-reads-per-alignment-start 0 \
+        --tmp-dir \$PWD \
         -I ${bam_file} \
         -O raw.vcf.gz
     
@@ -27,6 +28,7 @@ process MUTECT2 {
         -R ${reference} \
         --min-reads-per-strand 2 \
         -V raw.vcf.gz \
+        --tmp-dir \$PWD \
         -O ${bam_file.baseName}.vcf.gz
 
     bcftools norm \