config.yaml

# temporary storage
tmpdir : '/tmp'
# tmpdir : '/scratch'

#demux
barcodes : 'workflow/barcodes/TruSeq_400.fasta'

# deepvariant
DEEPVARIANT_VERSION : '1.5.0'
N_SHARDS            : 96

ref :
  shortname   : 'GRCh38_noalt'
  fasta       : 'reference/human_GRCh38_no_alt_analysis_set.fasta'
  index       : 'reference/human_GRCh38_no_alt_analysis_set.fasta.fai'
  chr_lengths : 'reference/human_GRCh38_no_alt_analysis_set.chr_lengths.txt'  # cut -f1,2 reference.fasta.fai > reference.chr_lengths.txt
  tr_bed      : 'workflow/aux/tandem_repeats.bed'
  exons       : 'workflow/aux/all_hg38_exons_ensembl.bed'

# glnexus
run_cohort: False
GLNEXUS_VERSION : 'v1.4.1'
merge : 1000000

# extra
QC :
  runQC  : False
  lowcov : 10

picard :
  near_distance : 5000
  sample_size   : 1000

pharmcat:
  run_analysis: True
  positions: 'workflow/aux/pharmcat_positions.vcf.bgz'
  mincov: 10

annotate:
    variants: 'annotation/00-All.fixed_chr_PGx_only.vcf.gz'
    gVCF: False