v4.0.0 - Chinese Baozi - [2026-06-27]
Breaking change
- #530 Updated AMPcombi, changed parameter
amp_ampcombi_cluster_removesingletonsintoamp_ampcombi_cluster_keepsingletons. (by @jasmezz, @jfy133)
Added
- #483 New screening workflow for CAZyme Gene Cluster (CGC) and substrate prediction, through dbCAN. (by @HaidYi)
- #483 Added support for preannotated input with optional GFF column in samplesheet for dbCAN CAZyme Gene Cluster (CGC) and substrate prediction, with new
--dbcan_skip_cgcand--dbcan_skip_substrateparameters. (by @HaidYi) - #500 Updated pipeline template to nf-core/tools version 3.4.1. (by @jfy133)
- #508 Added support for antiSMASH's --clusterhmmer, --fullhmmer, and --tigrfam options. (❤️ to @yusukepocky for requesting, @jfy133)
- #506 Added support GECCO convert for generation of additional files useful for downstream analysis. (by @SkyLexS)
- #507 Updated to nf-core template v3.5.1. (by @jfy133)
- #510 Fixed code to make Nextflow strict-syntax compliant. (by @jfy133)
- #521 Added option to turn on RGI's own cleanup of intermediate files. (❤️ to @SamD28 for requesting, added by @jfy133)
- #519 Added BiG-SLiCE (
bigslice) as a new BGC clustering tool in the BGC subworkflow. Activated with--bgc_run_bigsliceand requires--bgc_bigslice_db. (by @SkyLexS) - #528 Updated pipeline template to nf-core/tools version 4.0.2. (by @jfy133)
Fixed
- #501 Fixed issue with BAKTA HMMs not being staged correctly. (reported by @yusukepocky, fix by @jfy133)
Dependencies
| Tool | Previous Version | New Version |
|---|---|---|
| dbCAN | - | 5.2.9 |
| MultiQC | 1.27 | 1.34 |
| Bakta | 1.10.4 | 1.12.0 |
| BiG-SLiCE | - | 2.0.2 |
| nf-core | 3.3.2 | 4.0.2 |
| AMPcombi | 2.0.1 | 3.0.0 |
| GECCO | 0.9.10 | 0.10.1 |
Photo by Eason Lai from 上海, CC BY-SA 2.0 https://creativecommons.org/licenses/by-sa/2.0, via Wikimedia Commons
Contributors
jfy133, HaidYi, and 4 other contributors