Mercurial > repos > greg > vsnp_sample_names

diff vsnp_sample_names.xml @ 1:895d18fcfebe draft

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Uploaded
author greg
date Tue, 27 Oct 2020 18:21:55 +0000
parents f75e2ac7b6cd
children a56648c94fd3
line wrap: on
line diff
--- a/vsnp_sample_names.xml	Tue Apr 21 10:17:20 2020 -0400
+++ b/vsnp_sample_names.xml	Tue Oct 27 18:21:55 2020 +0000
@@ -4,7 +4,7 @@
 #import os
 #import re
 #set output_dir = 'output'
-mkdir -p $output_dir
+mkdir -p $output_dir &&
 #if str($input_type_cond.input_type) == "single":
     ## We may have a single read or a pair, but in
     ## either case we want the same base file name.
@@ -15,7 +15,7 @@
     #if $sample_name.find("_") > 0:
         #set sample_name = $sample_name.split("_")[0]
     #end if
-    echo $sample_name > $output
+    && echo '$sample_name' > '$output'
 #else:
     #for $i in $input_type_cond.reads_collection:
         #set sample_name = $os.path.basename($i.element_identifier)
@@ -23,7 +23,7 @@
             #set sample_name = $sample_name.split(".")[0]
         #end if
         #set output_file = $os.path.join($output_dir, $sample_name)
-        && echo $sample_name > $output_file
+        && echo '$sample_name' > '$output_file'
     #end for
 #end if
 ]]></command>