--- a/5_call_consensus.xml	Wed May 08 11:43:17 2019 -0400
+++ b/5_call_consensus.xml	Thu May 09 11:45:22 2019 -0400
@@ -2,17 +2,17 @@
     <description>for a sample, or lookup cached consensus SNP calls</description>
     <requirements>
         <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.7.3">python</requirement>
+        <requirement type="package" version="3.6.8">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
         #set $identifier = $call_pileup.name.split(' ')[0]
-        python3 $__tool_directory__/snp-cache.py snp_consenus_calls
+        python $__tool_directory__/snp-cache.py snp_consenus_calls
             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
             -c "
-                mkdir ./$identifier/
+                mkdir -p ./$identifier/
                 && cp $call_pileup ./$identifier/reads.all.pileup
                 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
             "
@@ -37,7 +37,7 @@
             <param name="snps" value="snplist.txt" />
             <param name="calls" value="samples/sample1/var.flt.vcf" />
             <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
-            <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" />
+            <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="20" />
             <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
         </test>
     </tests>