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Trim Galore v2.1.0-beta.3

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@github-actions github-actions released this 24 Apr 19:51
v2.1.0-beta.3
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Trim Galore v2.1.0-beta.3 — Oxidized Edition (beta)

Third beta of the Rust rewrite. Folds in three user-facing PRs merged since beta.2: help-text polish, pre-GA capability additions (A{N} shorthand, BGI auto-detect, Perl-parity fixes, rhetoric reframe), and the user-guide v2 refresh (plus two bugs it surfaced along the way).

New capabilities since v2.1.0-beta.2

  • BGI/DNBSEQ added to adapter auto-detection. Users running BGI/MGI/DNBSEQ data no longer need to pass --bgiseq explicitly; the 32 bp BGI adapter is now probed alongside Illumina, Nextera, and smallRNA on the first 1M reads. Stranded Illumina stays explicit-only (--stranded_illumina) because its sequence differs from Nextera by a single A-tail base and would produce constant ambiguous ties. Tie-break semantics unchanged — the zero-count fallback is still Illumina.
  • Repeatable -a / -a2 multi-adapter syntax. -a SEQ1 -a SEQ2 now works directly — no need for the v0.6.x embedded-string (-a " SEQ -a SEQ") or FASTA file workaround. Embedded-string and file:adapters.fa forms still work and can be mixed with repeated flags in a single invocation (e.g. -a " SEQ1 -a SEQ2" -a SEQ3).
  • Perl-style A{N} single-base expansion for -a / -a2 — e.g. -a A{10} expands to -a AAAAAAAAAA, matching Perl v0.6.x syntax.
  • Perl-era -r1 / -r2 / -a2 short-flag forms are accepted. Clap's single-character short-flag rule meant -r1 40 previously parsed as -r=1 with 40 becoming a stray positional (producing a confusing "odd count" error). A small pre-parse hook now transparently rewrites the exact tokens -r1, -r2, -a2 (and their =VALUE variants) to the existing --r1, --r2, --a2 long-alias forms so Perl-era scripts keep working.

Bug fixes since v2.1.0-beta.2

  • --trim-n is now suppressed under --rrbs, restoring Perl v0.6.x byte-identical output for users who combine both flags. Perl's RRBS code path omitted $trim_n from its Cutadapt invocations; beta.2 was applying N-trimming unconditionally, which narrowly violated the byte-identity guarantee for that specific flag combination.
  • Paired-end report line fix. The parameter-summary line in the text trimming report previously emitted a stray -end suffix (...before a sequence pair gets removed-end: 20 bp). Now correctly emits ...before a sequence pair gets removed: 20 bp. Single-end output is unchanged.

Documentation

  • Flag-by-flag help-text polish (#221). 25 docstring edits across src/cli.rs. --paired no longer claims "exactly 2 input files" (stale since beta.2's multi-pair fix); --rrbs help now warns against Tecan Ovation kit incompatibility; --small_rna surfaces its --length → 18 side-effect; --bgiseq notes it is also probed by auto-detection.
  • Positioning reframed from "byte-identical" to "faithful rewrite with useful additions" (#222). The original framing no longer held given new capabilities (poly-G handling, generic poly-A trimmer, per-pair adapter detection, BGI auto-detect). Updated in README, SUMMARY, User Guide, CHANGELOG, and the --help preamble.
  • User guide refreshed (#223). 534 → 325 lines. Dropped a ~220-line duplicate of --help that had been drifting out of sync on every polish cut; replaced with a curated "Flag reference" section on cross-flag interactions, RRBS-specific guidance (Tecan, MseI), and adapter-specification recap. Added IMPLICON coverage (missing from the original guide). Modernised the intro/framing.

Test coverage

Test count grew from 106 → 147 across the beta.2 → beta.3 window. New coverage: multi-pair validation branches, specialty modes (--clock, --implicon end-to-end), adapter brace expansion, four-probe auto-detection set, Perl-era flag rewriting, --trim-n / --rrbs interaction, parse_adapter_specs mixed-form path.

Install

Cargo

cargo install trim-galore --version 2.1.0-beta.3

Docker

docker pull ghcr.io/felixkrueger/trimgalore:v2.1.0-beta.3
# or the moving beta tag:
docker pull ghcr.io/felixkrueger/trimgalore:beta

Multi-arch OCI index digest: sha256:3d8e9c90555cb47176ea4f7527230c59995f402af6a32d3ef7b3428ca5d6b337 (linux/amd64 + linux/arm64).

Pre-built binaries

See the Assets section below for linux-x86_64, linux-aarch64, and macos-aarch64 archives with .sha256 checksums.

Feedback

Open an issue with the beta-feedback label, or continue the discussion at #215. Earliest GA is 2026-05-03.

Full changelog: v2.1.0-beta.2...v2.1.0-beta.3

Assets 8
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