anchor.diff:  % quality control
   qc = fastqc( fq: tag_fq ctl_fq );
   
  +fai = samtools-faidx( fa: fa );
  +
   % read mapping
   idx     = bowtie-build( fa: fa );
   tag_sam = bowtie-align( idx: idx, fq: tag_fq );
  
positive.code:   bedgraph = bamcoverage( bam: dedup_sorted_bam, bai: dedup_sorted_bai );
  }
  
  deftask bedtools-getfasta( bed_fa( File ) : fa( File ) bed( File ) )in bash *{
    bed_fa=$bed.fa
    bedtools getfasta -fi $fa -bed $bed -fo $bed_fa
  }*
  
  deftask restrict-peaks( restricted_bed( File ) : bed( File ) )in bash *{
    restricted_bed=$bed.100.bed
    perl -lane '$start=$F[1]-100 ; $end = $F[2]+100 ; print "$F[0]\t$start\t$end"' \
      $bed > $restricted_bed
  }*
  
  %% =========================================================
  %% INPUT DATA
  
negative.code: ctl_deeptools_bedgraph = deeptools( sam: ctl_sam );
  
  % extract fasta
  peaks_fa     = bedtools-getfasta( fa: fa, fai: fai, bed: peaks );
  
  % extend regions to 100 bps around the peak region and extract fasta
  peaks_100    = extend-peaks( bed: peaks );
  peaks_100_fa = bedtools-getfasta( fa: fa, fai: fai, bed: peaks_100 );
  
  
  %% =========================================================
  