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Trim Galore v2.1.0-beta.2

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@github-actions github-actions released this 20 Apr 13:48
v2.1.0-beta.2
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Trim Galore v2.1.0-beta.2 — Oxidized Edition (beta)

Second beta of the Rust rewrite. Folds in every improvement shipped since beta.1 two days ago, driven by beta-tester feedback (most importantly: multi-pair --paired is back).

New features (since v2.1.0-beta.1)

  • --version now prints build provenance on a second line: <git-hash> — <target> — built <ISO-8601 UTC timestamp>. The short -V remains one-line. Paste into bug reports to pin down an exact build.
  • Reproducible builds. Setting SOURCE_DATE_EPOCH to a fixed Unix timestamp (Debian reproducible-builds spec) produces a bit-identical binary across runs; unset behaviour is unchanged. Malformed values hard-fail the build.

Bug fixes (since v2.1.0-beta.1)

  • --paired accepts N pairs again. Common shell-glob invocations like trim_galore --paired *fastq.gz now work as they did in Perl v0.6.x. Adapter auto-detection and poly-G scanning run per pair — intentional deviation from v0.6.x, which detected once on the first file. Safer for mixed libraries / chemistries across a glob, negligible overhead.
  • Same-file R1/R2 detection. Paired-end validation catches byte-equal R1 and R2 paths (matches v0.6.x — no symlink resolution, no canonicalisation).
  • Cross-pair output-path collision pre-flight (fixes #216). Invocations that would silently overwrite one pair's output with another's abort before any I/O. Comparison is ASCII case-insensitive, so sample_R1.fq.gz and SAMPLE_R1.fq.gz collide correctly on APFS/NTFS (macOS/Windows default) as well as ext4.
    • On opt-in case-sensitive APFS/ZFS volumes, letter-case-distinct files are legitimately separate but the pre-flight will still reject them. Use distinct basenames or --basename per sample to work around.
    • On mid-batch failure at pair K, pairs 1..K−1 retain complete outputs and pair K may have a partial file; K+1..N are not attempted. Inspect and re-run only the failing pair — matches v0.6.x (no rollback).

Infrastructure (contributor-facing, no runtime effect)

  • New CI gates on every PR: cargo fmt --check + cargo clippy -D warnings (lint), a dedicated reproducibility job that builds twice under a fixed SOURCE_DATE_EPOCH and asserts bit-identity, and a weekly rustsec/audit-check for dependency advisories.
  • Dependabot enabled for cargo + github-actions ecosystems.

Install

Cargo

cargo install trim-galore --version 2.1.0-beta.2

Docker

docker pull ghcr.io/felixkrueger/trimgalore:v2.1.0-beta.2
# or the moving pointer:
docker pull ghcr.io/felixkrueger/trimgalore:beta

Pre-built binaries

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

Feedback

Beta testing feedback is the whole point of the window — please open an issue for anything surprising, or continue the discussion at #215. Earliest GA is 2026-05-03.

Full changelog: v2.1.0-beta.1...v2.1.0-beta.2

Assets 8
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