HLA typing (Short-read RNA)

HLA typing in short-read RNA sequencing BAM/FASTQ files

tools

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

arcashla, hlaminer, hlaprofiler, seq2hla, optitype

usage

nexus run --nf-workflow hla_typing_short-read-rna.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_short-read-rna
#
# Usage:
#   nextflow run hla_typing_short-read-rna.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
#   bam_file               (required for arcasHLA)
#   bam_bai_file           (required for arcasHLA)
#   fastq_file_1           (required for HLAProfiler, seq2HLA, OptiType)
#   fastq_file_2           (required for HLAProfiler, seq2HLA, OptiType)
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, arcashla, hlaminer, hlaprofiler, seq2hla, optitype
methods: "all"


# -----------------------------------------------------------------------------
# HLAminer (short-read RNA-seq)
# Optional arguments.
# -----------------------------------------------------------------------------
# Pipeline:
#   bwa aln/sampe (against HLAminer's coding 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"


# -----------------------------------------------------------------------------
# HLAProfiler
# Optional arguments.
# -----------------------------------------------------------------------------
hlaprofiler:
  # Extra CLI arguments passed directly to HLAProfiler predict.
  extra_args: "-allele_refinement all -if"


# -----------------------------------------------------------------------------
# seq2HLA
# Optional arguments.
# -----------------------------------------------------------------------------
seq2hla:
  # Extra CLI arguments passed directly to seq2HLA.
  extra_args: ""


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