Mercurial > repos > jpayne > snp_pipeline

changeset 19:4bb7e4a360bc

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planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
author jpayne
date Wed, 31 Jan 2018 12:38:03 -0500
parents 97abaa8b8384
children baf9ccfae6f0
files 6_merge_vcfs.xml 7_smp_matrix.xml
diffstat 2 files changed, 1 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/6_merge_vcfs.xml	Wed Jan 31 12:33:00 2018 -0500
+++ b/6_merge_vcfs.xml	Wed Jan 31 12:38:03 2018 -0500
@@ -1,7 +1,7 @@
 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
-        <!-- <requirement type="package" version="1.6">bcftools</requirement> -->
+        <requirement type="package" version="1.6">bcftools</requirement>
         <requirement type="package" version="1.0.6">bzip2</requirement>
         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
         <requirement type="package">tabix</requirement>
--- a/7_smp_matrix.xml	Wed Jan 31 12:33:00 2018 -0500
+++ b/7_smp_matrix.xml	Wed Jan 31 12:38:03 2018 -0500
@@ -8,11 +8,6 @@
         <requirement type="package" version="3.4">python3</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        env &&
-        which bcftools &&
-        which bunzip    &&
-        which snp-pipeline &&
-        which python   &&
         python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
             #for $fa in sorted($cons, key=lambda f: f.element_identifier)
                 -n $fa.element_identifier -f $fa