From cd51396b097cf63734578cdac8fc6c64500c8b4b Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 6 Aug 2024 07:58:12 +0200
Subject: [PATCH] fastqc: set tmpdir (#6207)

* fastqc: set tmpdir

xref https://github.com/galaxyproject/galaxy/pull/18628

* Update tools/fastqc/rgFastQC.xml

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

---------

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 tools/fastqc/rgFastQC.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/fastqc/rgFastQC.xml b/tools/fastqc/rgFastQC.xml
index 7c2bbf15cb4..f65263979fb 100644
--- a/tools/fastqc/rgFastQC.xml
+++ b/tools/fastqc/rgFastQC.xml
@@ -1,4 +1,4 @@
-<tool id="fastqc" name="FastQC" version="0.74+galaxy0">
+<tool id="fastqc" name="FastQC" version="0.74+galaxy1" profile="23.0">
     <description>Read Quality reports</description>
     <xrefs>
         <xref type="bio.tools">fastqc</xref>
@@ -50,6 +50,7 @@
                 --limits '${limits}'
             #end if
             --threads \${GALAXY_SLOTS:-2}
+            --dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} 
             --quiet
             --extract
             #if $min_length: