NBIS-Meta 2.3.2

Changelog:

• Update sourmash and contigtax versions
• Update and make sourmash database link configurable
• Add sourmash kmer size to config
• Better handling of one-sample data for Rscripts

NBIS-Meta 2.3.1

Changelog

• Fixed a bug where the prebuilt kraken database could not be unpacked properly due to varying subfolder depths inside the tar archive

NBIS-Meta 2.3

Changelog

• bugfixes for barrnap RNA prediction
• fixed a bug that forced use of MarkDuplicates with checkm profiling
• fixed a bug that removed first sample from checkm coverage
• removed more usage of opj for paths
• updated eggnog-mapper

NBIS-Meta 2.2

Changelog

• Add normalization of read counts using TMM, RLE and CSS (see Pereira et al 2018 benchmark)
• Replace (custom) calculation of TPM with RPKM calculation using edgeR
• Upgrade Resistance Gene Identifier to v5.1.1

Bugfixes

• Fix erroneous path to eggnog-parser.py script
• Fix KeyError when adding new units for samples

NBIS-Meta 2.1

Changelog

• Add configurability to genome filtering
• More checks for expected workflow output
• Fix default param settings using schema

NBIS-Meta 2.0

Version 2.0 of the NBIS-Metagenomics workflow.

This version includes among other things:

• a slimmed down core conda environment
• restructured workflow more in line with Snakemake template
• support for snakemake reports
• support for MetaPhlAn v3
• more genome binning support + QC with checkm, GTDB-TK and trRNA/rRNA counting.
• integrated SLURM profile support for running the workflow on clusters (e.g. Uppmax)