capellini.stages.preflight

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

Functions

run_preflight(cfg)

Create all output folders; if fresh_start is True wipe previous intermediates.
capellini.stages.preflight.run_preflight(cfg: CapelliniConfig) → None[source]

Create all output folders; if fresh_start is True wipe previous intermediates.

Protected files inside input_fasta_folder (never deleted):

  • virus FASTA

  • metadata file

Note: progenome16S.fasta is not protected — it lives bundled inside the package (capellini/data/references/) and the MMSeqs2 stage re-derives the working copy in input_fasta_folder automatically when needed.

Parameters:

cfg – Populated CapelliniConfig instance.