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