From cc18006a8ebfb67ad38b013af96ee8fce87d93be Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Tue, 27 Feb 2024 09:48:30 +0000
Subject: [PATCH] fix tempdir on HPC/singularity

---
 modules/local/score_report.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/local/score_report.nf b/modules/local/score_report.nf
index 8471ab30..0e1a3545 100644
--- a/modules/local/score_report.nf
+++ b/modules/local/score_report.nf
@@ -33,8 +33,9 @@ process SCORE_REPORT {
     run_ancestry = params.run_ancestry ? true : false
     """
     cp $projectDir/assets/report/report.qmd .
-    export DENO_DIR=\$(mktemp -d)
-    export XDG_CACHE_HOME=\$(mktemp -d)
+    mkdir quartotempdir
+    export DENO_DIR=\$(mktemp -d --tmpdir=quartotempdir)
+    export XDG_CACHE_HOME=\$(mktemp -d --tmpdir=quartotempdir)
 
     echo $workflow.commandLine > command.txt
     echo "keep_multiallelic: $params.keep_multiallelic" > params.txt