.config.yaml

# tbpore external tools parameters config file
# DO NOT EDIT - parameters that should be changed by users are listed in the program options
# these are parameters that are passive to be changed, so they are listed here

mykrobe:
  predict:
    params: "--ont --format json --min_proportion_expected_depth 0.20 --species tb -m 2048MB"

rasusa:
  params: "-g 4411532 -s 88"

decom_DB:
  url: "https://github.com/mbhall88/tbpore#configuring-the-decontamination-database-index"

minimap2:
  map_to_decom_DB:
    params: "-aL2 -x map-ont"
  map:
    params: "-a -L --sam-hit-only --secondary=no -x map-ont"

samtools:
  sort_decom_DB:
    params: ""
  index_decom_DB:
    params: ""
  sort:
    params: ""

filter_contamination:
  params: "--verbose --ignore-secondary"

extract_decontaminated_nanopore_reads:
  params: "grep"

sort_decontaminated_reads:
  params: "sort"

stats:
  params: "-vv -s"

bcftools:
  mpileup:
    params: "-x -I -Q 13 -a 'INFO/SCR,FORMAT/SP,INFO/ADR,INFO/ADF' -h100 -M10000"
  call:
    params: "--ploidy 1 -V indels -m"

filter:
  params: "-P --verbose --overwrite"
  verbose_params:
    min_depth:       5
    min_fed:         0.2
    max_depth:       0
    min_qual:        25
    min_strand_bias: 1
    min_bqb:         0
    min_mqb:         0
    min_rpb:         0
    max_sgb:         0
    min_vdb:         0.00001
    min_mq:          30
    min_frs:         0.90

consensus:
  params: "--verbose --ignore all --het-default none"

psdm:
  params: "--ignore-case --quiet --sort"

decontamination_db:
  url:                 "https://figshare.com/ndownloader/files/36708444"
  compressed_sha256:   "f9b66d7a5410455199702a77d45f57625ddd0418f81d3ba8a8369781c56187cc"
  decompressed_sha256: "8677817748e9d76c19eb888230dfd4eebff51105dfb15d1f0c02e8361cd21001"