Curare

Changed
- `--cores` option is now mandatory
- DESeq2 fold changes are now inversed, so that edgeR and DESeq2 results are comparable
- Count tables for DESeq2 get rounded, so `--fraction` of featureCounts will work with DESeq2

Added
- New modules
- HISAT2
- Differential gene expression with edgeR
- Curare wizard now supports download of RefSeq genomes and annotations
- STAR index and STAR mapping now have threads options. These can be used to control how many mappings can run in parallel
- DESeq2 and edgeR modules also visualize the gene body coverage (using RSeQC)

Fixed
- Fixed STAR index bug: Errors during STAR index building could lead to a state where Curare thought that the index was build properly
- A chromosome column was missing in DGE summary xlsx files

Fixed (1 change)
- Fixed error during version parsing with newer conda/mamba versions

Changed (7 changes)
- Curare uses conda/mamba by default and "--use-conda" is changed to "--no-conda"
- Update of all tool versions
- Update Snakemake to 7.32.3
- All Curare modules now use fixed versions (Conda dependencies use '=', not '>=')
- Tidied up correlation heatmap in 'dge_analysis'
- Reworked 'dge_analysis' parameters: Options for using 'Parent' in GFFs as ID (useful when working with exons)
- All modules will now generate csi files instead of bai files (This allows Curare to work with large plant genomes)

Added (5 changes)
- New modules
- bwa-mem2
- minimap2
- fastp
- Curare wizards now warns if target files already exist
- "--keep-going" option: If a module throws an error, independent modules will still finish

Fixed (5 changes)
- Fixed wrong mapped reads counting in STAR
- Fixed error with xgzipped files
- Fixed 'multiqc' error when Curare was rerun in same directory
- Fixed clustering bug in 'dge_analysis' for cases with >65,536 genes
- Standardized order of samples in all visualization

Fixed (1 change)
- Fixed bug in dge_analysis xlsx converter

Fixed (1 change)
- Fixed broken PyPI build (snakefiles and report folder will now also be installed)

Added (1 change)
- Made Curare PyPI and Bioconda ready
- All executives are now also found under ./bin and can this way be easliy added to your PATH

Changed (1 change)
- Renamed "curare_env.yml" to "conda_environment.yaml" for a more meaningful name