HLA typing (Long-read DNA)

HLA typing in long-read DNA sequencing FASTQ files

tools

The following tools run by default (methods: "all"):

fufihla, hlaminer, spechla, specimmune

usage

nexus run --nf-workflow hla_typing_long-read-dna.nf -params-file params.yaml

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

Download params.yaml

# =============================================================================
# params.yaml — hla_typing_long-read-dna
#
# Usage:
#   nextflow run hla_typing_long-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             long-read DNA 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, fufihla, hlaminer, spechla, specimmune
methods: "all"


# -----------------------------------------------------------------------------
# FuFiHLA
# Optional arguments.
# -----------------------------------------------------------------------------
fufihla:
  # Extra CLI arguments passed directly to fufihla. Use --hifi for PacBio HiFi
  # or --ont for Oxford Nanopore.
  extra_args: "--hifi"


# -----------------------------------------------------------------------------
# HLAminer (long-read DNA)
# Optional arguments.
# -----------------------------------------------------------------------------
# Pipeline:
#   minimap2 (against HLAminer's genomic HLA reference) | HLAminer.pl
hlaminer:
  # 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. Long reads need
  # relaxed thresholds. Common flags:
  #   -i <minimum percent identity>
  #   -s <minimum alignment score>
  #   -q <minimum log10 expect value>
  hlaminer_extra_args: "-s 500 -q 1 -i 1"


# -----------------------------------------------------------------------------
# SpecHLA (long-read)
# Optional arguments.
# -----------------------------------------------------------------------------
spechla:
  # Extra CLI arguments passed directly to spechla-long-read.
  extra_args: ""


# -----------------------------------------------------------------------------
# SpecImmune
# Optional arguments.
# -----------------------------------------------------------------------------
specimmune:
  # Extra CLI arguments passed directly to SpecImmune (scripts/main.py).
  #   -i  typing target:        HLA | KIR | CYP | IG_TR | extend
  #   -y  read type:            nanopore | pacbio | pacbio-hifi
  #   --seq_tech  library type: wgs | amplicon  (DNA/WGS is the default mode;
  #               do NOT pass an RNA token here — use --RNA_type for RNA data)
  extra_args: "-i HLA -y pacbio-hifi --seq_tech wgs"