# HG changeset patch
# User greg
# Date 1700777468 0
# Node ID d2ac1f5c05ed2a89c94dcd52e1e21d8f492053fc
# Parent  0fd0a757072c913f0a8b92cd57d8dfab755cc692
Uploaded

diff -r 0fd0a757072c -r d2ac1f5c05ed cfsan_snp_pipeline_call_consensus_snps.xml
--- a/cfsan_snp_pipeline_call_consensus_snps.xml	Wed Nov 22 22:12:50 2023 +0000
+++ b/cfsan_snp_pipeline_call_consensus_snps.xml	Thu Nov 23 22:11:08 2023 +0000
@@ -5,8 +5,8 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-#set $identifier = $input_call_pileup.element_identifier
-mkdir -p ./$identifier/ &&
+#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' &&