Curare 0.6.0

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

Curare 0.5.1

Fixed

• Fixed error during version parsing with newer conda/mamba versions

Curare 0.5.0

Changed

• 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

• 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

• 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

Curare 0.4.5

Fixed (1 change)

• Fixed a bug in dge_analysis' xlsx converter

Curare 0.4.4

Fixed (1 change)

• Fixed broken PyPI build (snakefiles and report folder will now also be installed)

Curare 0.4.3

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

Curare 0.4.2

0.4.2

Added (1 change)

• Add "Normalized Coverage" module to Analysis

Fixed (1 change)

• Fix broken "Normalized Coverage" added by mistake last release

Curare 0.4.1

Fixed (1 change)

• Fix old heading "Groups" to "Samples" in report (Report)

Curare 0.4.0

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)

Curare 0.3.1

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)