Mercurial > repos > iuc > bwa_mem2

diff bwa-mem2.xml @ 6:d459a463cb73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 05dbd4644d6c63d6404d1c79ba1d0b6000807ca5
author iuc
date Fri, 28 Mar 2025 15:51:05 +0000
parents fea76fc17330
children bec6ba059ded
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--- a/bwa-mem2.xml	Fri Mar 28 08:29:39 2025 +0000
+++ b/bwa-mem2.xml	Fri Mar 28 15:51:05 2025 +0000
@@ -116,9 +116,9 @@
 #end if
 
 #if str( $output_sort ) == "coordinate":
-        | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
+        | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -m "\${GALAXY_MEMORY_MB_PER_SLOT:-768}M" -O bam -o '$bam_output'
 #elif str( $output_sort ) == "name":
-        | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
+        | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -m "\${GALAXY_MEMORY_MB_PER_SLOT:-768}M" -O bam -o '$bam_output'
 #else
         | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
 #end if