A small pipeline that takes SARS-CoV-2 consensus sequences, aligns them against a reference genome while constraining
the length of the alignment to match the lenght of the reference genome (using mafft --keeplength). After alignment,
the 5' and 3' untranslated regions (UTRs) are trimmed.
nextflow run BCCDC-PHL/consensus-align-utr-trim \
[--ref <path_to_ref_genome>] \
--run_dir <path_to_run_dir>