HLA typing (Short-read)

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

tools

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

arcashla, hlaprofiler, seq2hla

usage

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


# -----------------------------------------------------------------------------
# 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: ""