Overview

Parameters

--hml
  • HML file
  • Required parameter
--output
  • Output directory
  • Required parameter
--imgtdir
  • Location of where the BLAST IMGT database is located
  • Default location is /opt/html on the docker container
--imgt
  • IMGT database version
  • Default is 3200
--report
  • Binary flag for generating HTML validation report
  • default is 1

Executing

./nextflow run nmdp-bioinformatics/flow-blast-hml -with-docker \
        nmdpbioinformatics/docker-blast-hml \
        --hml test_file.hml --outdir /path/to/output/dir

After running this command you should find a report and a validated file in the ouput directory you specified.