Mercurial > repos > sanbi-uwc > novo_align

changeset 26:709eb84d9927 draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 7e0e4d01725950cee2d1cc4d4384a258fdb3937b
author sanbi-uwc
date Mon, 07 May 2018 06:44:07 -0400
parents 5aa122947f26
children df170f4d2eea
files novo_align.xml
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/novo_align.xml	Mon May 07 06:06:13 2018 -0400
+++ b/novo_align.xml	Mon May 07 06:44:07 2018 -0400
@@ -68,7 +68,11 @@
                     #end if
                 #end if
             #else
-                --forward_file ${fastq_in}.${fastq_in.ext} --reverse_file ${fastq_in}.${fastq_in.ext}
+                #if $fastq_in.metadata.is_gzipped
+                    --forward_file ./input_singles.gz.${fastq_in.ext} --reverse_file ./input_singles.gz.${fastq_in.ext}
+                #else
+                    --forward_file ./input_singles.${fastq_in.ext} --reverse_file ./input_singles.${fastq_in.ext}
+                #end if
             #end if
 
     ]]></command>