minor fixes

mfiers · Jun 18, 2012 · 66d46c4 · 66d46c4
1 parent ead2afc
commit 66d46c4
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Showing 2 changed files with 4 additions and 7 deletions.
diff --git a/template2/recursive_map.jinja2 b/template2/recursive_map.jinja2
@@ -61,3 +61,7 @@ lasti=0
 samtools mpileup -uf $lastreference ${bamfiles} \
     | bcftools view -cg - \
     | vcfutils.pl vcf2fq > final.consensus.fq
+
+
+echo "Convert the fq output to contigs - for postprocessing"
+fastq2contigs  final.consensus.fq final.contigs.fasta
diff --git a/template2/soapdenovo_postprocess.jinja2 b/template2/soapdenovo_postprocess.jinja2
@@ -74,11 +74,4 @@ $DEBUG time GapCloser -a $lastScaff \
 $DEBUG fastaInfo -O -s -i {{ output }} length ncount scaf1 scaf10 scaf100 \
     > 9.final.stats
 
-echo "And now start a Hagfish run with the libraries"
-echo "Create bowtie database"
-bowtie-build {{ output }} hagfishdb
-
-mkdir hagfish_bam
-{% for l in fq_forward %}
-bowtie -p {{ threads }}