Mercurial > repos > jpayne > snp_pipeline

changeset 39:1fe3b14f7f1b

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 14 Feb 2018 13:06:44 -0500
parents a057e69d13a7
children 02733e77f84f
files 1_map_reads.xml 4_merge_sites.xml
diffstat 2 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Mon Feb 05 13:25:39 2018 -0500
+++ b/1_map_reads.xml	Wed Feb 14 13:06:44 2018 -0500
@@ -7,6 +7,7 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        env &&
         #if $reads.reads_select == 'collection'
             export files="$reads.coll.forward $reads.coll.reverse"          &&
             export params="-1 $reads.coll.forward -2 $reads.coll.reverse"   &&
--- a/4_merge_sites.xml	Mon Feb 05 13:25:39 2018 -0500
+++ b/4_merge_sites.xml	Wed Feb 14 13:06:44 2018 -0500
@@ -25,10 +25,10 @@
         <test>
             <param name="calls">
                 <collection type="list">
-                    <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" />
-                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" />
-                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" />
-                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" />
+                    <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
                 </collection>
             </param>
             <!-- <output name="snplist" value="snplist.txt" /> -->