Mercurial > repos > greg > affy_ids_for_genotyping

changeset 1:85da3036bd6a draft

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Uploaded
author greg
date Tue, 04 Dec 2018 14:32:07 -0500
parents b37deda778b9
children a70f103aed16
files affy_ids_for_genotyping.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/affy_ids_for_genotyping.xml	Tue Dec 04 14:20:10 2018 -0500
+++ b/affy_ids_for_genotyping.xml	Tue Dec 04 14:32:07 2018 -0500
@@ -1,9 +1,9 @@
 <tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0">
     <description>from VCF data</description>
     <command detect_errors="exit_code"><![CDATA[
-grep "#CHROM" '$input_vcf' > test.head
-tr '\t' '\n' < test.head > samples.txt
-sed -i 1,9d samples.txt
+grep "#CHROM" '$input_vcf' > test.head &&
+tr '\t' '\n' < test.head > samples.txt &&
+sed -i 1,9d samples.txt &&
 awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output'
 ]]></command>
     <inputs>