sv_tools.yaml

tools_enabled_methods:
  - "lumpy"
  - "manta"
  - "svaba"
  - "naibr"
  - "grocsvs"
  - "longranger"
  - "pbsv"
  - "sniffles"


tools_read_type_to_method:
  illumina: 
    - "lumpy"
    - "manta"
    - "svaba"
  linked:
    - "naibr"
    - "grocsvs"
    - "longranger"
  long:
    - "pbsv"
    - "sniffles"

tools_methods_conda_dir: "conda" # FIX with full path if ran from outside the master dir


tools_methods:
  sniffles:
    path: "sniffles"
    threads: 15
    max_num_splits: 10
    max_distance: 1000
    min_length: 30
    num_reads_report: -1
    min_seq_size: 1000
    min_support: 2
    conda: "sniffles.yaml"
    support_cnt_script:
      path: "scripts/support_cnt_filter_sniffles.py" # FIX with full path if ran from outside the master dir
      conda: "support_cnt.yaml"
      python: "python"
  pbsv:
    path: "pbsv"
    conda: "pbsv.yaml"
    support_cnt_script:
      path: "scripts/support_cnt_filter_pbsv.py" # FIX with full path if ran from outside the master dir
      conda: "support_cnt.yaml"
      python: "python"
  lumpy:
    path: "lumpyexpress"
    conda: "lumpy.yaml"
    extract_script: extractSplitReads_BwaMem
    samtools:
      path: "samtools"
  manta:
    config_script: configManta.py
    mode: local
    threads: 15
    conda: "manta.yaml"
  grocsvs:
    path: "/path/to//grocsvs" # FIX with real path. NOT RELATED TO CONDA, MUST BE INSTALLED SEPARATELY
    cluster_type: "multiprocessing"
    processes: 15
    conda: "grocsvs.yaml"
    idba_ud:
      path: "/path/to/idba_ud"  # FIX with real path. NOT RELATED TO CONDA. MUST BE INSTALLED SEPARATELY
    samtools: 
      path: "samtools"
    tabix:
      path: "tabix"
    bgzip:
      path: "bgzip"
    bwa:
      path: "bwa"
  rck:
    conda: "rck.yaml"
    rck_adj_x2rck:
      path: "rck-adj-x2rck"
    rck_adj_process:
      path: "rck-adj-process"
    rck_adj_rck2x:
      path: "rck-adj-rck2x"
    rck_adj_stats:
      path: "rck-adj-stats"
    rck_adg_infer:
      path: "rck-adg-infer"
    rck_adg_process:
      path: "rck-adg-process"
    call_set_script:
      path: ""
  naibr:
    conda: "naibr.yaml"
    python:
      path: "python"
    script:
      path: "/path/to/NAIBR-master/NAIBR.py" # FIX with real path. NOT RELATED TO CONDA. MUST BE INSTALLED SEPARATELY
    min_mapq: 40
    threads: 8
  svaba:
    conda: "svaba.yaml"
    path: "/path/to/svaba/bin/svaba" # fIX with real path
    threads: 15
  survivor:
    conda: "survivor.yaml"
    path: "SURVIVOR"
  reads_stats:
    path: "scripts/read_lengths_stats.py" # FIX if not running from the master dir
    conda: "reads_stats.yaml"
    python: "python"
    median: True
    N50: True
    min_truncated_length: 1500
    max_truncated_length: 1000000000