project_name : "test"
project_dir : "test/test_project/"
sequencing_runs : 
  - name : "Run1"
    version : 'v1'
    dir : "test/seq_runs/run_v1_single_file"
    fastq_path : "{read}.fastq.gz"
    library_name : "test_lib0"
  - name : "Run2"
    version : 'v2'
    dir : "test/seq_runs/run_v2_single_file"
    fastq_path : "{read}.fastq.gz"
    library_name : "test_lib1"
  - name : "Run3"
    version : 'v2'
    dir : "test/seq_runs/run_v2_split"
    fastq_path : "{library_prefix}_{split_affix}_{read}_001.fastq.gz"
    split_affixes : ["L001", "L002"]
    libraries : 
      - {library_name: "test_lib1", library_prefix: "lib1"}
      - {library_name: "test_lib2", library_prefix: "lib2"}
  - name : 'Run4'
    version : 'v3'
    dir : "test/seq_runs/run_v3"
    fastq_path : "Undetermined_S0_{split_affix}_{read}_001.fastq.gz"
    split_affixes : ["L001", "L002"]
    libraries : 
      - {library_name: "test_lib3", library_index: "ATAGAG"}
      - {library_name: "test_lib4", library_index: "AGAGGA"}
paths : 
  bowtie_index : "/Users/averes/Projects/Melton/grch38_test/Homo_sapiens.GRCh38.85.annotated"
  python_dir : "/Users/averes/miniconda3/envs/py27/bin/"
  samtools_dir : "/Users/averes/software/samtools-1.3.1/bin/"
  rsem_dir : ""
  java_dir : ""
parameters : # OPTIONAL 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
#     low_complexity_mask: False
#   bowtie_arguments:
#     m : 200
#     n : 1
#     l : 15
#     e : 1000
  trimmomatic_arguments:
    LEADING: "28"
    SLIDINGWINDOW: "4:20"
    MINLEN: "16"
