anchor.diff:  }
   
   deftask per-fastq( sortedbam : fa( File ) [fastq1( File ) fastq2( File )] db( File ) ) {
  -  sam = bowtie2-align(
  +  sam = bwa-align(
       idx:    bt2idx
       fastq1: fastq1
       fastq2: fastq2 );
  
positive.code: db = '<%= node[:hiway][:variantcall][:annovardb][:directory] %>/<%= node[:hiway][:variantcall][:annovardb][:file] %>';
  
  // (3) Workflow Definition
  bt2idx = bowtie2-build( fa: fa );
  fai = samtools-faidx( fa: fa );
  fun exonicfun = per-chromosome(
    fa:     fa
  
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 *{
  