Issue

Due to an oversight, the convenience parameters --clip_r1, --clip_r2, --three_prime_clip_r1, --three_prime_clip_r2 that instruct Trim Galore to trim the respective number of bases from the reads are not used, even when specified by the user. In rare cases, this may lead to slightly lower mapping rates.

Resolution

This regression was not fixed. The parameters were removed from the pipeline in version 3.11 to avoid confusion. Since then, tool-specific trimming and other arguments can be provided via the --extra_trimgalore_args respectively the --extra_fastp_args.