old_contents: from pypipe.tools import bwa, bowtie2, samtools, bcftools
  
  ref = Fasta("GRCh37.fa", check=False)
  pipeline.add_file(ref)
  bwa_i = BwaIndex("GRCh37.fa", check=False) 
  pipeline.add_file(bwa_i)
  i = Bowtie2Index("GRCh37", check=False)
  pipeline.add_file(i)
  r1 = Fastq("IonXpress_021.fastq", check=False)
  pipeline.add_file(r1)
  r2 = Fastq("IonXpress_022.fastq", check=False)
  pipeline.add_file(r2)
  
  sam1 = bowtie2.bowtie2(_x=i, _U=[r1], _S="out1.sam", _p=4, log="bowtie_log")
  pipeline.draw('img1.svg')
  bam1 = samtools.view(in_=sam1, _o="out1.bam", _b=True, _S=True)
  pipeline.draw('img2.svg')
  s_bam1 = samtools.sort(in_=bam1, out="sorted1")
  pipeline.draw('img3.svg')
  
  sam2 = bwa.bwasw(ref=bwa_i, in1=r2, out="out2.sam", log="bwa_log")
  pipeline.draw('img4.svg')
  bam2 = samtools.view(in_=sam2, _o="out2.bam", _b=True, _S=True)
  pipeline.draw('img5.svg')
  s_bam2 = samtools.sort(in_=bam2, out="sorted2")
  pipeline.draw('img6.svg')
  
  bcf = samtools.mpileup(in_=[s_bam1, s_bam2], out="out.bcf", _u=True, _f=ref)
  pipeline.draw('img7.svg')
  vcf = bcftools.view(in_=bcf, out="out.vcf")
  pipeline.draw('img8.svg')
  
new_contents: from pypipe.tools import bwa, bowtie2, samtools, bcftools
  
  ref = Fasta("GRCh37.fa")
  bwa_i = BwaIndex("GRCh37.fa") 
  i = Bowtie2Index("GRCh37")
  r1 = Fastq("IonXpress_021.fastq")
  r2 = Fastq("IonXpress_022.fastq")
  
  sam1 = bowtie2.bowtie2(_x=i, _U=[r1], _S="out1.sam", _p=4, log="bowtie_log")
  bam1 = samtools.view(in_=sam1, _o="out1.bam", _b=True, _S=True)
  s_bam1 = samtools.sort(in_=bam1, out="sorted1")
  
  sam2 = bwa.bwasw(ref=bwa_i, in1=r2, out="out2.sam", log="bwa_log")
  bam2 = samtools.view(in_=sam2, _o="out2.bam", _b=True, _S=True)
  s_bam2 = samtools.sort(in_=bam2, out="sorted2")
  
  bcf = samtools.mpileup(in_=[s_bam1, s_bam2], out="out.bcf", _u=True, _f=ref)
  vcf = bcftools.view(in_=bcf, out="out.vcf")
  
subject: Correct example file