0.6.1 Software updates and new features

see the Changelog: https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2024-06-19-version-061

0.6.0 Bug fixes and updates

see the Changelog: https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2024-01-29-version-060

0.5.1 Bug fixes

see the Changelog: https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2023-03-07-version-051

0.5.0 Bug fixes and updates

see the Changelog: https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2023-02-15-version-050

0.4.2 Bug fixes

Updates related to large genome sizes and/or large sample sizes:

• Run snpEff with option to specify -Xmx for large genomes and add the rules to cluster.yaml
• Fix y-axis labels for mutational load plot so that there is no overlap for large sample sizes
• Create new Docker images with bedtools and htslib (bgzip) so that VCF files filtered with bedtools can be compressed in a pipe to reduce intermediate file sizes

Minor bug fixes:

• Update conda in GitHub actions to reduce run time
• Shorten run time and lower number of cores for mutational load calculations in cluster.yaml
• Remove temp flag from bam index file of rescaled bam files
• Embed pipeline logo into GenErode pipeline report via link to file on repository so that the pipeline report can be moved to a different location
• Fix "rerun incomplete" warning for rule make_reference_bed by separating it from the group job reference_prep_group

see https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2022-09-05-version-042

0.4.1 First public release of GenErode

This is the first public version of GenErode, a Snakemake pipeline that analyzes whole genome re-sequencing data from ancient/historical and modern samples.