diff --git a/src/cutadapt/cli.py b/src/cutadapt/cli.py index d8abb6d8..2b0ba16c 100644 --- a/src/cutadapt/cli.py +++ b/src/cutadapt/cli.py @@ -1105,11 +1105,13 @@ def make_adapter_cutter( def make_shortener(length1: Optional[int], length2: Optional[int], paired: bool): if paired: if length1 is not None and length2 is not None: + # If -l and -L are given, shorten both reads. yield Shortener(length1), Shortener(length2) elif length1 is not None and length2 is None: - # If -L not given, use same setting for both - yield Shortener(length1), Shortener(length1) + # If only -l is given, shorten read 1. + yield Shortener(length1), None elif length1 is None and length2 is not None: + # If only -L is given, shorten read 2. yield None, Shortener(length2) else: if length1 is not None: