Mercurial > repos > iuc > umi_tools_dedup

diff umi-tools_dedup.xml @ 9:1692b1acebfd draft

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"planemo upload commit 5d3fc4232e0e036ac1ed9e2c36adc41d6af4987f"
author iuc
date Tue, 10 Sep 2019 14:28:24 -0400
parents a6477bafd522
children c6567483aa1e
line wrap: on
line diff
--- a/umi-tools_dedup.xml	Tue Aug 27 17:11:11 2019 -0400
+++ b/umi-tools_dedup.xml	Tue Sep 10 14:28:24 2019 -0400
@@ -34,7 +34,7 @@
                 --in-sam
             #end if
             -I '$input_file' -S deduped.bam &&
-            samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM
+            samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />