Hard-trimming

--hardtrim5 and --hardtrim3 are run-and-exit modes that hard-clip every read to a fixed length, then exit. They run before quality and adapter trimming and don't touch report output.

Hard-trimming to leave bases at the 5' end

--hardtrim5 INT clips reads down to their first INT bases. Output goes to {stem}.{INT}bp_5prime.fq(.gz). Useful for shortening reads to a uniform length:

before:         CCTAAGGAAACAAGTACACTCCACACATGCATAAAGGAAATCAAATGTTATTTTTAAGAAAATGGAAAAT
--hardtrim5 20: CCTAAGGAAACAAGTACACT

Hard-trimming to leave bases at the 3' end

--hardtrim3 INT keeps only the last INT bases. Output goes to {stem}.{INT}bp_3prime.fq(.gz). Useful for removing a fixed bias at the 5' end (e.g. UMIs or inline barcodes):

before:         CCTAAGGAAACAAGTACACTCCACACATGCATAAAGGAAATCAAATGTTATTTTTAAGAAAATGGAAAAT
--hardtrim3 20:                                                   TTTTTAAGAAAATGGAAAAT

When to use this

Hard-trimming is a sledgehammer: quality is ignored, adapters are ignored, every read is clipped to the same length. It's the right tool for:

• Standardising read lengths for tools that require fixed-length input.
• Removing a known fixed bias at one end (e.g. UMI or inline barcode) before passing data through a second Trim Galore run for adapter and quality trimming.
• Producing equally-sized inputs for benchmarking.

For everything else, prefer the fine-grained --clip_R1, --clip_R2, --three_prime_clip_R1, --three_prime_clip_R2 flags, which apply on top of normal quality and adapter trimming.

Compatibility

Both modes accept multiple input files in a single invocation and process them sequentially. Paired-end mode is not required. --hardtrim* operates per-file independently.

--hardtrim5 and --hardtrim3 cannot be combined in one invocation; to apply both, run two passes and feed the first trim's output to the second.

Output files are named from the input's basename alone and written to the current working directory (or --output_dir if given), never beside the input. Two inputs sharing a basename therefore collide even when they come from different directories, and the run is refused before anything is written.