hlaminer-lr-dna

Profile HLA alleles from long-read DNA FASTQ files using

usage

nexus run --nf-workflow hla_typing_hlaminer-lr-dna.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_minimap2 "-ax map-hifi --secondary=no" \
    --params_hlaminer "-s 500 -q 1 -i 1"

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

parameter	description
`--samples_tsv_file`	TSV file with the following columns: ‘sample_id’, ‘fastq_file’.
`--output_dir`	Directory to which output files will be copied.
`--params_minimap2`	minimap2 extra CLI parameters (default: ‘“-ax map-hifi `--secondary`=no”’). Use -ax map-hifi for PacBio HiFi reads, or -ax map-ont for Oxford Nanopore reads. Note that the parameters need to be wrapped in quotes.
`--params_hlaminer`	HLAminer.pl extra CLI parameters (default: ‘“-s 500 -q 1 -i 1”’). Long reads need relaxed thresholds; the default mirrors HLAminer’s official long-read WGS demo (HPRAwgs_ONT*). Common flags include -i -s -q Note that the parameters need to be wrapped in quotes.