anchor.diff:  db = '<%= node[:hiway][:variantcall][:annovardb][:directory] %>/<%= node[:hiway][:variantcall][:annovardb][:file] %>';
   
   // (3) Workflow Definition
  -bt2idx = bowtie2-build( fa: fa );
  +bt2idx = bwa-build( fa: fa );
   fai = samtools-faidx( fa: fa );
   fun exonicfun = per-chromosome(
     fa:     fa
  
positive.code: }
  
  deftask per-fastq( sortedbam : fa( File ) [fastq1( File ) fastq2( File )] db( File ) ) {
    sam = bowtie2-align(
      idx:    bt2idx
      fastq1: fastq1
      fastq2: fastq2 );
  
negative.code: 
  deftask samtools-sort( sortedbam( File ) : bam( File ) )in bash *{
    sortedbam=alignment-sorted.bam
    samtools sort -m `expr <%= node[:hiway][:variantcall][:memory_mb] %> \* 512 \* 1024` $bam alignment-sorted
  }*
  
  deftask samtools-mpileup( mpileup( File ) : sortedbam( File ) [fa( File ) fai( File )] )in bash *{
  