# HG changeset patch
# User greg
# Date 1700691170 0
# Node ID 0fd0a757072c913f0a8b92cd57d8dfab755cc692
# Parent  3275d4866650d9502ad87ac532ab984fb051060f
Uploaded

diff -r 3275d4866650 -r 0fd0a757072c cfsan_snp_pipeline_call_consensus_snps.xml
--- a/cfsan_snp_pipeline_call_consensus_snps.xml	Fri Oct 13 17:57:44 2023 +0000
+++ b/cfsan_snp_pipeline_call_consensus_snps.xml	Wed Nov 22 22:12:50 2023 +0000
@@ -5,7 +5,10 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-cfsan_snp_pipeline call_consensus -v 4 -l '$input_merged_snp_sites' --vcfFileName 'consensus.vcf' '$input_call_pileup' &&
+#set $identifier = $input_call_pileup.element_identifier
+mkdir -p ./$identifier/ &&
+cp '$input_call_pileup' ./'$identifier'/reads.all.pileup &&
+cfsan_snp_pipeline call_consensus -v 4 -l '$input_merged_snp_sites' --vcfFileName 'consensus.vcf' ./'$identifier'/reads.all.pileup 1>&2 &&
 mv ./consensus.fasta '$output_fasta' &&
 mv ./consensus.vcf '$output_vcf'
     ]]></command>