anchor.diff:  deftask bowtie2-build( idx( File ) : fa( File ) )
   in bash *{
     bowtie2-build $fa bt2idx
  +  idx=idx.tar
     tar cf $idx --remove-files bt2idx.*
   }*
   
  
positive.code: 
  % varscan
  deftask varscan( vcf( File ) : mpileup( File ) )in bash *{
    varscan mpileup2snp $mpileup --output-vcf --p-value 99e-02 > $vcf
  }*
  
  
negative.code: : idx( File ) [fastq1( File ) fastq2( File )] )in bash *{
  
    tar xf $idx
    bam=alignment.bam
    bowtie2 -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 --no-unal -x bt2idx \
    -1 $fastq1 -2 $fastq2 -S - | samtools view -b - > $bam
    rm bt2idx.*
  