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nf-core / bacass

Simple bacterial assembly and annotation pipeline
https://nf-co.re/bacass
MIT License
60 stars 41 forks source link

Single end Illumina processing? #82

Open limey-bean opened 1 year ago

limey-bean commented 1 year ago

Is there a way to process single end reads with bacass? I am attempting to modify config files, and it would be amazing if you already had a solution in hand.

Best, Emily

d4straub commented 1 year ago

Unfortunately short read single end data isnt working with bacass. FW & RV read need to be present in order to be parsed here, and single_end=false is hardcoded here. It seems here it was planned to support SE data but then it wasnt. So it wont be enough to modify configs, the input sheet parsing is not made for single end data.