v1.6.0

• updated yaml files (--from-history export), fixed pandas v2 issues (peakachu, deeptools) and sortmerna upgrade
• BS mode BAM tag and flag tweaks
• BAM de-duplication with UMIs fixed
• improved volcano plot y-axis labels
• peakachu and salmon calls improved
• PCA plots with ellipses, faceted or arranged for additional factor
• SGE module made memory aware
• download support for GSE accession numbers and technical SRA reads
• bedgraph support for bigwig::apply
• standalone alignment::sizeselect
• use condabin directory for shared binaries across envs

v1.5.0

improvements on

• peak calling (min widths, further optimized for cut&tag, up/down sampling bam for spikein normalization)
• variant calling (speedup and padding)
• BS methylation rates inference (haarz on BWA, methyldackel on segemehl)
• vcf and bam indices are now created on the fly
• improved UMI representation in bam
• slicing fixed if no. seq <= threads
• refactored dlgenome and added new bundles to download (GATK, dbSNP)

v1.4.0

• revised error bubbling and locking in activate.sh script, added completions
• helper::multijoin / helper::join is now parallelized
• new bigwig::apply function to calculate statistics via datamash from multiple files in a record-wise parallelized fashion
• GNU parallel now leverages on a custom shell, that re-activates bashbone and/or conda
• extended genomic data download by orthologs
• upgrade and adaption to patched tools (bgzip #1767, rapidgzip #36, dupsifter #3, gztool #20)
• enhanced usages