# =============================================================================
# params.yaml — hla_typing_short-read-dna
#
# Usage:
#   nextflow run hla_typing_short-read-dna.nf -params-file params.yaml
#
# Fill in the required fields below. Optional fields can be left at their
# defaults or removed entirely.
# =============================================================================


# -----------------------------------------------------------------------------
# Required
# -----------------------------------------------------------------------------

# TSV file with columns:
#   sample_id
#   fastq_file_1           paired-end short-read FASTQ (read 1), gzipped
#   fastq_file_2           paired-end short-read FASTQ (read 2), gzipped
samples_tsv_file: ""

# Directory to which output files will be copied
output_dir: ""


# -----------------------------------------------------------------------------
# Optional — general
# -----------------------------------------------------------------------------

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, hlaminer, optitype, spechla
methods: "all"


# -----------------------------------------------------------------------------
# HLAminer (short-read DNA)
# Optional arguments.
# -----------------------------------------------------------------------------
# Pipeline:
#   bwa aln/sampe (against HLAminer's genomic HLA reference) | HLAminer.pl
hlaminer:
  # Extra CLI arguments passed directly to "bwa aln" (run per mate).
  bwa_aln_extra_args: "-e 0 -o 0"

  # Extra CLI arguments passed directly to "bwa sampe" (pairing step).
  bwa_sampe_extra_args: "-o 1000"

  # Extra CLI arguments passed directly to HLAminer.pl. Short reads keep the
  # strict default identity/expect thresholds. Common flags:
  #   -i <minimum percent identity>
  #   -s <minimum alignment score>
  #   -q <minimum log10 expect value>
  hlaminer_extra_args: "-s 500"


# -----------------------------------------------------------------------------
# OptiType
# Optional arguments.
# -----------------------------------------------------------------------------
optitype:
  # Extra CLI arguments passed directly to OptiType. Use --dna for DNA data.
  extra_args: "--dna"


# -----------------------------------------------------------------------------
# SpecHLA (short-read)
# Optional arguments.
# -----------------------------------------------------------------------------
spechla:
  # Extra CLI arguments passed directly to spechla. Use -u 0 for full-length
  # (WGS) data or -u 1 for exome/RNA data.
  extra_args: ""