Mercurial > repos > marcoalbuquerque > bam_parallelism_test

changeset 4:0ec6a49b43df draft

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Uploaded
author marcoalbuquerque
date Mon, 02 Mar 2015 20:03:55 -0500
parents a26d456c51dd
children 44005870d0f3
files bam_parallelism_test.xml
diffstat 1 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/bam_parallelism_test.xml	Mon Mar 02 20:01:11 2015 -0500
+++ b/bam_parallelism_test.xml	Mon Mar 02 20:03:55 2015 -0500
@@ -5,13 +5,15 @@
 	<parallelism method="multi" split_inputs="interval" split_mode="by_rname" real_split="False" merge_outputs="output"/>
 	<command>
 
-		samtools view $normal \$(cat $interval) | head -n 5 > $output;
-		samtools view $tumour \$(cat $interval) | head -n 5 >> $output;
+		ln -s $normal input.bam
+		ln -s $normal.metadata.bam_index input.bam.bai
+
+		samtools view input.bam \$(cat $interval) | head -n 5 > $output;
 
 	</command>
 	<inputs>
 		<param type="data" format="bam" name="normal" label="Normal Alignment BAM"/>
-		<param type="data" format="bam" name="tumour" label="Tumour Alignment BAM"/>
+
 		<param type="data" format="txt" name="interval" label="Interval File"/>
 	</inputs>
 	<outputs>