Mercurial > repos > artbio > lumpy_smoove

diff macro_lumpy_smoove.xml @ 2:49a8a327cc72 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"
author artbio
date Wed, 26 Aug 2020 05:48:01 -0400
parents ee8fc44b1655
children
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line diff
--- a/macro_lumpy_smoove.xml	Tue Aug 25 12:48:08 2020 -0400
+++ b/macro_lumpy_smoove.xml	Wed Aug 26 05:48:01 2020 -0400
@@ -6,8 +6,8 @@
         ln -s '${reference_source.ref_file}' reference.fa &&
         samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
     #else:
-        ln -s '${source.index.fields.path}' reference.fa &&
-        ln -s '${source.index.fields.path}.fai' reference.fa.fai &&
+        ln -s '${reference_source.index.fields.path}' reference.fa &&
+        ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai &&
     #end if
     ]]></token>