capellini.stages.preflight

Pre-flight stage: folder initialization and optional fresh-start cleanup.

Functions

run_preflight(cfg)

Create all output folders; if fresh_start=True delete previous intermediates.

capellini.stages.preflight.run_preflight(cfg: CapelliniConfig) → None[source]

Create all output folders; if fresh_start=True delete previous intermediates.

Protected files (never deleted):

virus FASTA in input_fasta_folder
bundled progenome16S.fasta (if present)
metadata file

Parameters:: cfg – Populated CapelliniConfig instance.