anchor.diff:  : 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.*
  
positive.code: deftask bowtie2-build( idx( File ) : fa( File ) )
  in bash *{
    bowtie2-build $fa bt2idx
    tar cf $idx --remove-files bt2idx.*
  }*
  
  
negative.code: 
  % varscan
  deftask varscan( vcf( File ) : mpileup( File ) )in bash *{
    vcf=variants.vcf
    varscan mpileup2snp $mpileup --output-vcf --p-value 99e-02 > $vcf
  }*
  
  