specimmune

Profile HLA / KIR / CYP / IG-TR alleles from long-read FASTQ files using SpecImmune

usage

nexus run --nf-workflow hla_typing_specimmune.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_specimmune "-i HLA -y pacbio-hifi --seq_tech rna --RNA_type traditional"

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_specimmune	SpecImmune (scripts/main.py) extra CLI parameters (default: ‘“-i HLA -y pacbio”’). Use -i to select the typing target (HLA | KIR | CYP | IG_TR | extend). Use -y to select the read type (nanopore | pacbio | pacbio-hifi). Note that the parameters need to be wrapped in quotes.