ReleaseNotes

v0.1.8 — 2026-01-03

Fixed a bug in the plot title naming logic that resulted in all plots having as title the first sample name present in the summary file.
Fixed some typos in the README.
Fixed the default number of threads that was not correctly working for HPC environments.

Made BAM input files positional arguments.
Slightly updated the sequencing saturation plot.
Thanks to @ewels for adding a new YAML output file which contains all data in a single file. It also contains run metadata: date, tool version, options etc. for reproducibility and future MultiQC support. An example here.
Thanks to @ewels again for some CLI teaks: docstrings for CLI functions, to give intro text; metavars in the help string, to avoid wide column due to –genome options; moved the tool subcommands above –help and –version. Finally, replaced static panel with dynamic Rich progress bar.
Due to the restructuring above, now methurator plot command takes in input the methurator_summary.yml file, to avoid calculating again the sequencing saturation curve.

Removed --bamdir option: if you want to specify more than 1 bam file within a directory you can now simply use the same --bam option, specifying all bam files (e.g. –bam files/*.bam)
Added Bioconda and Biocontainer instructions on the README.
Added the –rrbs parameter: if specified (by default), it will add the –keepDups flag to MethylDackel to avoid removal of duplicates.

methurator — a Python package for estimating sequencing saturation in bisulfite sequencing data. Read the README file for more information.