paths : 
  bowtie_dir : ''
  rsem_dir : ''
  python_dir : ''
  java_dir : ''
  samtools_dir : ''
parameters : 
  umi_quantification_arguments:
    m : 10 #Ignore reads with more than M alignments, after filtering on distance from transcript end.
    u : 1 #Ignore counts from UMI that should be split among more than U genes.
    d : 600 #Maximal distance from transcript end, NOT INCLUDING THE POLYA TAIL
    split-ambigs: False #If umi is assigned to m genes, add 1/m to each gene's count (instead of 1)
    min_non_polyA: 15 #Require reads to align to this much non-polyA sequence. (Set to 0 to disable filtering on this parameter.)
  output_arguments:
    output_unaligned_reads_to_other_fastq: False
    filter_alignments_to_softmasked_regions: False
  bowtie_arguments:
    m : 200
    n : 1
    l : 15
    e : 80
  trimmomatic_arguments:
    LEADING: "28"
    SLIDINGWINDOW: "4:20"
    MINLEN: "16"
    argument_order: ['LEADING', 'SLIDINGWINDOW', 'MINLEN']
  low_complexity_filter_arguments:
    max_low_complexity_fraction : 0.50
