# =============================================================================
# params.yaml — hla_typing_long-read
#
# Usage:
#   nextflow run hla_typing_long-read.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             long-read FASTQ (PacBio or Nanopore), 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-lr-rna, specimmune
methods: "all"


# -----------------------------------------------------------------------------
# HLAminer (long-read RNA-seq)
# Optional arguments.
# -----------------------------------------------------------------------------
# Pipeline:
#   minimap2 (against HLAminer's HLA CDS reference) | HLAminer.pl
hlaminer-lr-rna:
  # Extra CLI arguments passed directly to minimap2 for the upstream
  # alignment step. Use -ax map-hifi for PacBio HiFi, -ax map-ont for ONT.
  minimap2_extra_args: "-ax map-hifi --secondary=no --MD"

  # Extra CLI arguments passed directly to HLAminer.pl. Common flags:
  #   -e <expect value threshold>
  #   -s <minimum alignment score>
  #   -q <minimum mapping quality>
  #   -i <minimum percent identity>
  hlaminer_extra_args: "-e 1 -s 500 -q 1 -i 1"


# -----------------------------------------------------------------------------
# SpecImmune
# Optional arguments.
# -----------------------------------------------------------------------------
specimmune:
  # Extra CLI arguments passed directly to SpecImmune (scripts/main.py).
  # Use -i to select the typing target: HLA | KIR | CYP | IG_TR | extend
  # Use -y to select the read type:     nanopore | pacbio | pacbio-hifi
  extra_args: "-i HLA -y pacbio-hifi --seq_tech rna --RNA_type traditional"