Mercurial > repos > marcoalbuquerque > bam_parallelism_test

changeset 1:213289565e12 draft

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Uploaded
author marcoalbuquerque
date Sat, 28 Feb 2015 19:35:41 -0500
parents ab54013c8203
children 6ec7c93b90a6
files bam_parallelism_test.xml
diffstat 1 files changed, 1 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/bam_parallelism_test.xml	Sat Feb 28 19:29:43 2015 -0500
+++ b/bam_parallelism_test.xml	Sat Feb 28 19:35:41 2015 -0500
@@ -5,11 +5,7 @@
 	<parallelism method="multi" split_inputs="normal,tumour" split_mode="by_rname" real_split="False" merge_outputs="output"/>
 	<command>
 
-		{
-		samtools view -H $normal;
-		samtools view $normal \$(echo interval.txt) | head -n5;
-		samtools view $tumour \$(echo interval.txt) | head -n5;
-		} | samtools view -bS - > $output;
+		cat interval.txt;
 
 	</command>
 	<inputs>