Curare

Added (1 change)
- Add "Normalized Coverage" module to Analysis

Fixed (1 change)
- Fix broken "Normalized Coverage" added by mistake last release

Fixed (1 change)
- Fix old heading "Groups" to "Samples" in report (Report)

Added (2 change)
- Curare now supports new mapping modules:
- STAR
- Bowtie

Changed (1 change)
- All preprocessing modules will now gzip fasta files. This allows the removal of the gunzip module and 100% support of gzipped fastq files.

Fixed (1 change)
- Min/Max values in the setting should be inclusive: min <= value <= max (Pipeline)

Added (1 change)
- Added option for strand specificity of reads to features (DGE Analysis)

Changed (1 change)
- Bowtie2 alignment mode (local/end-to-end) is now optional and by default "end-to-end"

Fixed (1 change)
- Fixed incorrect usage of local alignment mode with paired-end datasets (Bowtie2)

Added (5 change)

- Added main GFF feature to assignment chart title (Report - DGE Analysis & Count Table)
- Added button for opening the original count table (Report - DGE Analysis & Count Table)
- Added button for opening the DESeq2 comparison directory (Report - DGE Analysis)
- Added pagination on tables (Report)
- Added summary about mapping tool parameters (Report - Mapping)

Changed (3 changes)

- Allowlist for GFF feature was created. If another feature is required, use 'ADDITIONAL_FEATCOUNTS_FEATURES' (DGE Analysis Module).
- Allowlist: "CDS", "exon", "intron", "gene", "mRNA", "tRNA", "rRNA", "ncRNA", "operon", "snRNA", "snoRNA", "miRNA", "pseudogene", "small regulatory ncRNA", "rasiRNA", "guide RNA", "siRNA", "stRNA", "sRNA"
- Tabs were replaced with dropdown menus (Report)
- Runtime notation on overview page now in hours, minutes and seconds (Report)

Fixed (3 change)
- Fixed broken header anchors on overview page (Report)
- Fixed incorrect curare dependencies
- Fixed unused Segemehl parameters

Added (3 changes)

- Added mamba support and made mamba default when using conda
- Added support of gff.gz files (DGE Analysis Module)
- Added 'N' (None) option at module selection (Curare Wizard)

Fixed (4 changes)

- Fixed bug when all options in a module are optional
- Fixed parsing errors of pipeline and samples file
- Check and create missing output folders
- Use curare snakefiles folder as a default (Curare Wizard)

Changed (1 change)

- Changed '--attribute' list from space-separated to comma-separated (DGE Analysis Module)