2.2.0: Merge pull request #122 from nf-core/dev

v2.2.0 nf-core/bacass: "Aqua Platinum Zebrafish" 2024/03/27

Changed

• #111 - Update nf-core/bacass to 2.12, and #117 to 2.13.1 TEMPLATE.

Added

• #104, #106 - Added dragonflye module and enbled draft genome polishing with short-reads.

Fixed

• #123 - Add fallback to download_pipeline.yml when the pipeline does not support stub runs (#2846)

Dependencies

• #120 - Update local and nf-core modules (version update an minnor code changes).

Tool	Previous version	New version
Bakta	1.8.2	1.9.3
Canu	2.2	-
Dragonflye	1.1.2	-
Fastp	0.23.4	-
Kraken2	2.1.2	-
Miniasm	0.3_r179	-
Minimap2	2.2	2.24
Nanoplot	1.41.6	-
Porechop	0.2.4	-
Prokka	1.14.6	-
Quast	5.2.0	-
Racon	1.4.20	-
Samtools	1.17	1.19.2
Untar	1.34	-
Dfast	1.2.20	-
Medaka	1.4.3-0	-
Nanopolish	0.14.0	-
PycoQC	2.5.2	-
Unicycler	0.4.8	-

Deprecated