v0.4

• added preprocessing of raw reads
• added --preprocessed flag to suppress preprocessing for already preprocessed datasets
• R1/R2 read lengths are now assessed and homogenised separately (i.e. they can have different lengths as supported by Figaro)
• initial read length distribution assessment is now performed by fastqc
• fastq filenames are normalised to R1/R2 naming scheme
• readlen homogenisation is now performed by bbduk
• added mapseq-profiling of asv sequences
• added two parameters (--dada2_chimera_method, --dada2_chimera_min_fold_parent_over_abundance) for dada2 chimera removal

Bugfixes/Workarounds

• fixed an R script error that would generate the wrong table format when having a single sample
• in dada2_analysis commented vortex-code (prevalence check) as it fails for certain samples

v0.3

• added single-end library support
• restructured to proper nextflow structure (dropped Python-package structure)
• added Singularity definition
• various fixes