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wodanaz / Assembling_viruses

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Prompt for trim adapter type #47

Open johnbradley opened 3 years ago

johnbradley commented 3 years ago

Currently we only trim nextera adapters from the input fastq.gz files using the --nextera flag: https://github.com/wodanaz/Assembling_viruses/blob/ccff5c0c2cd535016b083670b4fceeae824afd1e/scripts/remove-nextera-adapters.sh#L19

Add a prompt so users can specify what type of adapter trimming to perform.

See adapter trimming documentation for trim_galore.