anchor.diff:  
   deftask bwa-align( bam( File ) : idx( File ) [fq1( File ) fq2( File ) group] )in bash *{
     tar xf $idx
  +  bam=aligned_reads.bam
     bwa mem -R "@RG\tID:group${group}\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1" bwaidx $fq1 $fq2 -t 4 | samtools view -b - > $bam
   }*
   
   % Picard tools
   deftask picard-sort( sortedbam( File ) : bam( File ) )in bash *{
  +  sortedbam=sorted.bam
     picard SortSam I=$bam O=$sortedbam SO=coordinate
   }*
   
   deftask picard-merge( mergedbam( File ) : <bam( File )> )in bash *{
  +  mergedbam=merged.bam
     picard MergeSamFiles I=$bam SO=coordinate AS=true O=$mergedbam
   }*
   
  
positive.code: 
  deftask picard-dict( dict( File ) : fa( File ) )in bash *{
    ln -s $fa ref.fa
    picard CreateSequenceDictionary REFERENCE=ref.fa OUTPUT=$dict
  }*
  
  deftask picard-bai( bai( File ) : bam( File ) )in bash *{
    picard BuildBamIndex I=$bam O=$bai
  }*
  
  
negative.code: 
  % gunzip
  deftask gunzip( out( File ) : gz( File ) )in bash *{
    out=unzipped_${gz%.gz}
    gzip -c -d $gz > $out
  }*
  
  