Mercurial > repos > iuc > umi_tools_group

diff umi-tools_group.xml @ 10:a24f5b991320 draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:27:38 -0400
parents f73f13641bb6
children 30c3906fbf43
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line diff
--- a/umi-tools_group.xml	Tue Aug 27 17:10:29 2019 -0400
+++ b/umi-tools_group.xml	Tue Sep 10 14:27:38 2019 -0400
@@ -38,7 +38,7 @@
             #end if
             --output-bam
             -I '$input_file' -S grouped.bam &&
-            samtools sort grouped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM
+            samtools sort grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" />