Minimal set of files and directories expected in the working directory.
NE_nCoV_rapid/
│
├── pre-analyses/
├── provision.json → FASTA file with the latest genomes from GISAID
├── new_genomes.fasta → FASTA file with newly sequenced genomes
├── metadata_nextstrain.tsv → metadata downloaded from GISAID
└── Sequencing.xlsx → Custom lab metadata file