Mercurial > repos > cstrittmatter > skesa

changeset 3:c546fef7fd13 draft

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Uploaded
author estrain
date Wed, 15 Aug 2018 09:32:37 -0400
parents 2f4443bea09d
children 15be58c254f5
files skesa.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/skesa.xml	Mon Aug 13 20:19:27 2018 -0400
+++ b/skesa.xml	Wed Aug 15 09:32:37 2018 -0400
@@ -6,13 +6,13 @@
     #if $jobtype.select != "cl"
 	skesa
       #if $jobtype.select == "asm"
-        -i ${draft.name}.fasta
+        -i $draft
       #else if $jobtype.select == "se"
-        --fastq ${fastq1.name}.fastq
+        --fastq $fastq1.name
       #else if $jobtype.select == "pe"
-	--fastq ${fastq1.name}.fastq,${fastq2.name}.fastq
+	--fastq $fastq1.name,$fastq2 --use_paired_ends
       #end if
-	--use_paired_ends > results.skesa.fasta
+	> results.skesa.fasta
     #end if 
 
     ]]></command>