Mercurial > repos > jjohnson > optitype

diff optitype.xml @ 1:bd817c1fdd63 draft

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Uploaded
author jjohnson
date Wed, 23 Sep 2015 15:35:45 -0400
parents 887bc9c92c05
children 61fc10014a9e
line wrap: on
line diff
--- a/optitype.xml	Thu Aug 27 17:07:26 2015 -0400
+++ b/optitype.xml	Wed Sep 23 15:35:45 2015 -0400
@@ -24,8 +24,10 @@
   ln -s "${fastq_input.fastq_input1}" reads.fastq
   #set $fastqs = ['reads.fastq']
 #end if
+&& cp \$OPTITYPE_DIR/config.ini .
+&& ln -s \$OPTITYPE_DIR/data data
 #set $input_fq = ' '.join($fastqs)
-&& python OptiTypePipeline.py 
+&& python  \$OPTITYPE_DIR/OptiTypePipeline.py 
 $read_type --input  ${' '.join($fastqs)}
 #if $beta != None: 
  --beta $beta
@@ -33,7 +35,7 @@
 #if $enumerate != None: 
  --enumerate $enumerations
 #end if
---output $outdir
+--outdir $outdir
 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
 && cp $outdir/*/*_result.tsv $result
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