2.3 - Flowering Orchards

Added

• #237 Added Euclidian distance/z-score info to report text/heatmaps; added tables next to heatmaps in case the heatmap plotting does not work
• #229 Added param for clustering (or not) the heatmaps
• #226 Added logic to read newer multiqc files from rnaseq 3.12
• #225 Added param for pathway analysis datasources
• #221 Added padj to volcano hovertext

Changed

• #244 Release 2.3 to master, part II (found a bug before actual release)
• #237 Changed geom_jitter to geom_point for volcano plot so that points are accurate
• #233 Release 2.3 to master, part I
• #225 Shortened names of some output files

Fixed

• #243 Fix missing QBiC logo and css styling in report by adding logo/css params
• #242 Fix path issue in report by adding report_file/references_file params
• #241 Undo fix branch protection bug in order to get precommit test to run
• #240 Fix branch protection bug --> third attempt
• #239 Fix branch protection bug --> second attempt
• #238 Fix branch protection bug
• #237 Fix version in usage docs and remove duplicate datasources in test_custom_gmt.config
• #236 Fixed new multiqc check (in case both the files of the old and new mqc version are present)
• #234 Fixed unnecessary file permission changes from #225
• #228 Fixed text in report
• #229 Fixed cutoff enrichment plot labels, fixed wrong plotMA function being called (also fixed this changelog)
• #225 Fixed too many devices error from tryCatch around normalized heatmaps
• #221 Fixed non-conformable arrays bug, fix wrong volcano colors when no DE genes