hlaminer-sr-dna

Profile HLA alleles from short-read DNA FASTQ files using HLAminer

usage

nexus run --nf-workflow hla_typing_hlaminer-sr-dna.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_bwa_aln "-e 0 -o 0" \
    --params_bwa_sampe "-o 1000" \
    --params_hlaminer "-s 500"

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_1’, ‘fastq_file_2’.
`--output_dir`	Directory to which output files will be copied.
`--params_bwa_aln`	bwa aln extra CLI parameters (default: ‘“-e 0 -o 0”’). Note that the parameters need to be wrapped in quotes.
`--params_bwa_sampe`	bwa sampe extra CLI parameters (default: ‘“-o 1000”’). Note that the parameters need to be wrapped in quotes.
`--params_hlaminer`	HLAminer.pl extra CLI parameters (default: ‘“-s 500”’). Mirrors HLAminer’s official short-read demo (HPRAwgs_classI-II.sh); short reads keep the strict default identity/expect thresholds. Common flags include -i -s -q Note that the parameters need to be wrapped in quotes.