mag 2.0.0 - Silver Swan

• Switch to Nextflow DSL2
• Changed --input file format from TSV to CSV format, requires header now
• Add BUSCO automated lineage selection functionality
• Add taxonomic bin classification with GTDB-Tk
• Add process for CAT database creation as an alternative to using pre-built databases
• Allow different folder structures for Kraken2 databases
• Requires nextflow version >= 21.04.0

See full CHANGELOG, for more information.

mag 1.2.0 - Yellow Squirrel

• Manifest file has to be handed over via --input parameter now
• Changed format of manifest input file: requires a '.tsv' suffix and additionally contains group ID
• Add --coassemble_group parameter to allow group-wise co-assembly
• Add --binning_map_mode parameter allowing different mapping strategies to compute co-abundances used for binning
• TSV --input file allows now also entries containing only short reads

See full CHANGELOG, for more information.

mag 1.1.2 - Blue Panda

• Fixed processing of --input parameter

See full CHANGELOG, for more information.

mag 1.1.1 - Lime Owl

• Add full-size test
• Add worfklow overview figure to README
• Fix seaborn to v0.10.1 to avoid nanoplot error

See full CHANGELOG, for more information.

mag 1.1.0 - White Elephant

• Add host read removal with Bowtie 2
• Add separate MultiQC section for FastQC after preprocessing
• Add MetaBAT2 RNG seed parameter --metabat_rng_seed and set the default to 1 which ensures reproducible binning results
• Add parameters --megahit_fix_cpu_1, --spades_fix_cpus and --spadeshybrid_fix_cpus to ensure reproducible results from assembly tools
• Fixed channel joining for multiple samples causing MetaBAT2 error
• Compress assembly files
• Fix BUSCO errors

See full CHANGELOG, for more information.

mag 1.0.0 - Purple Corgi

First release of the MAG pipeline 🎉

This initial version of the pipeline:

• assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/
• performs assembly using https://github.com/voutcn/megahit and http://cab.spbu.ru/software/spades/, and checks their quality using http://quast.sourceforge.net/quast
• performs metagenome binning using https://bitbucket.org/berkeleylab/metabat/src/master/, and checks the quality of the genome bins using https://busco.ezlab.org/