mhcflurry2-scan

Predict antigen presentation using MHCflurry 2.0

usage

nexus run --nf-workflow antigen_prediction_mhcflurry2-scan.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --alleles "" \
    --params_mhcflurry2_predict_scan ""

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’, ‘csv_file’.
--alleles	Alleles to predict.
--output_dir	Directory to which output files will be copied.
--params_mhcflurry2_predict_scan	mhcflurry-predict-scan parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.