1.5.0

• Implemented sylph. This is an additional module for species-level metagenomic profiling.
• Fixed a possible error exit in the assembly process MERGE_MAG_ABUNDANCE.
• Improved input checks for csv file and SRA inputs.
• SRA file downloads should now be much more stable.
• The pipeline won't terminate the whole run when a sample cannot be assembled.
• README now contains a quick start guide
• Adjusted RAM requirements for processes

1.4.0

• New name: TOFU-MAaPO
• Added SRA download function
• Every run will produce a used software version list
• Added Salmon and a 'salmon only'-workflow
• Added fastp to the qc (optional)
• Added co-assembly support
• Added semibin2
• Support for freely choosing the binner tools to use in an assembly workflow
• Added the full magscot scoring outputs to the published results
• Added Checkm bin quality table to outputs
• Checkm is now skipable
• Setting Metaphlan within HUMAnN to run in offline mode
• Setting FASTQC to run only on two cores

1.3.2

• Fixed an issue that let CONCOCT crash

• Introducing subgrouping for Vamb for big cohorts

• Results are now published together in specific folders

• Updated usage docs, updated configs for kiel medcluster, misc cleaning

• Adding docs for installation and custom config, fixing updating metaphlan and humann processes to create dir if not yet present

• adding gtdbtk update database process

• fixing the metaphlan db version to the one hardcoded by humann

• metagenomic-workflows is now TOFU-MAaPO

• adding overview picture of currently available modules

1.3.1

• Updated medcluster configs
• Vamb workflow can now create subgroups of samples. This is a fix for large cohorts that will lead to large intermediate files that might crash the pipeline.
• Updated docs

1.3.0

-Adding extended genome assembly module including the bin-refinement tool MAGScoT.
-Updating Metaphlan and Humann
-Updating config for medcluster: Adding new file storage system
-Usage of more external containers to reduce dependency stress within the default container

1.2.2

Updated GTDB-Tk to version 2.1.0 which results in a reduction of memory requirements.

1.2.1

Added functionality to skip QC-Module to continue with already QC'ed reads.

1.2.0

Added possibility to use a csv table in --reads. Needed are columns 'id', 'read1' and in the case of paired-reads 'read2'. File needs to be comma-separated.
Added --single_end parameter to enable single-end reads mode.

1.1.2

kraken2 now uses both reads in paired-end runs

1.1.1

Switch to Docker