Nextflow wrapper for ktmeaton/ncov-recombinant
This pipeline is designed to take in the run name, the ncov2019-artic-nf output directory of consensus sequence files for that run and the corresponding metadata.tsv file as input.
nextflow run BCCDC-PHL/ncov-recombinant-nf \
-profile conda \
--cache ~/.conda/envs \
--artic_analysis_dir </path/to/artic-outputs> \
--run_name <run_name> \
--metadata </path/to/metadata.tsv> \
--outdir </path/to/outdir>