seqwish fails when --output-dir contains commas

[kdm9]

Hi folks,

Seqwish interprets commas in a PAF file path as multiple PAF files. This causes havoc when one uses commas in the --output-dir of PGGB (for example I used a dir like pggb_s5000_p90_G700,1000 encoding the pggb params in the dir name).

I'd suggest adding a check to the pggb script to ensure that output & tmp paths don't contain commas. Happy to implement this if you need.

best,
K

[subwaystation]

If you really need this, please make a PR @kdm9, thanks!