Allow user to force writing outputs into existing output directory

BCCDC-PHL / FluViewer

Tool for generating influenza A virus genome sequences from FASTQ data

https://bccdc-phl.github.io/FluViewer/

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Allow user to force writing outputs into existing output directory #29

Closed jpalmer37 closed 3 months ago

jpalmer37 commented 3 months ago

Currently, fluviewer will fail if you give it the command line parameter --outdir . because it already exists. This was implemented to prevent overwrites of existing result folders.

Since the overwrite check is a safe design choice, I don't necessarily want to remove it. I am considering whether we could solely skip an overwrite check if outdir is the present working dir (.) and check any other outputs like normal. Open to suggestions.

dfornika commented 3 months ago

How about this? We add a --force flag that allows the user to specify that they want to proceed with analysis even if the outdir already exists.

dfornika commented 3 months ago

Fixed in #30