Example Nextflow nomenclature pipeline

This pipeline is an example for genomic nomenclature (using https://github.com/phac-nml/genomic_address_service).

A write-up of this pipeline is at phac-nml/nf-pipelines#1.

If you have Nextflow and Docker installed, you can test it out with:

nextflow run apetkau/nf-core-genomicnomenclature -profile docker,test -r dev -latest --outdir results

Or, if you wish to use your own data:

nextflow run apetkau/nf-core-genomicnomenclature -r dev -latest -profile docker --input profilesheet.csv --outdir results

Here, the profilesheet.csv lists the cg/wgMLST profiles to cluster/generate nomenclature. The format is a CSV file that contains the columns: id, profiles_format, allele_profiles. An example is below (or refer to the test profilesheet.csv).

profilesheet.csv:

id	profiles_format	allele_profiles
test	tsv	allele_profiles.tsv

Output for genomic address mcluster will be in results/genomic/{id}_results, which contains the output of gas mcluster as described at https://github.com/phac-nml/genomic_address_service.