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"