curare - 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

- Python
Published by pblumenkamp about 2 years ago

curare - Curare 0.5.1

Fixed

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

- Python
Published by pblumenkamp over 2 years ago

curare - 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

- Python
Published by pblumenkamp over 2 years ago

curare - Curare 0.4.5

Fixed (1 change)

• Fixed a bug in dge_analysis' xlsx converter

- Python
Published by pblumenkamp almost 4 years ago

curare - Curare 0.4.4

Fixed (1 change)

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

- Python
Published by pblumenkamp about 4 years ago

curare - 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 "curareenv.yml" to "condaenvironment.yaml" for a more meaningful name

- Python
Published by pblumenkamp about 4 years ago

curare - 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

- Python
Published by pblumenkamp about 4 years ago

curare - Curare 0.4.1

Fixed (1 change)

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

- Python
Published by pblumenkamp about 4 years ago

curare - 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)

- Python
Published by pblumenkamp about 4 years ago

curare - 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)

- Python
Published by pblumenkamp over 4 years ago

curare - Curare 0.3

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 'ADDITIONALFEATCOUNTSFEATURES' (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

Fixed (3 change)

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

- Python
Published by pblumenkamp over 4 years ago

curare - Curare 0.1.1

Removed (1 change)

• removed unneeded keep file in DESeq2 summary.

Changed (1 change)

• switched from not normalized to normalized counts in DESeq2 summary.

- Python
Published by pblumenkamp almost 5 years ago

curare - Curare 0.2.2

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 default (Curare Wizard)

Changed (1 change)

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

- Python
Published by pblumenkamp almost 5 years ago

curare - Curare 0.2.1

Added (1 change)

• Added conditions file for GenExVis (DGE-Analysis).

Fixed (1 change)

• Fixed missing column name for Gene IDs in normalized count table (DGE-Analysis).

- Python
Published by pblumenkamp over 5 years ago

curare - Curare 0.2

Added (9 changes)

• Added a Wizard (curare_wizard.py) for creating samples and pipeline file.
• Added a cluster mode for send long-running steps to a cluster node as a job (--cluster-comand, --cluster-config-file, --cluster-nodes). If using cluster mode, the latency-wait parameter should be increased (--latency-wait in seconds).
• Added a final report summarizing all used software and the most important results.
• Added bwa (http://bio-bwa.sourceforge.net/) as a mapping module. This includes the bwa-backtrack bwa-mem and bwa-sw algorithm.
• Added conda support for automatically installing all dependencies for each module.
• Added more detailed error messages when DESeq2 analyses terminate. Now, the module prints if and which R package is missing.
• Added new visualizations to differential expression analysis.
• Added Segemehl as an additional mapping module.
• Added Trim Galore for data preprocessing.

Fixed (2 changes)

• Fixed a bug in which the DESeq2 R script would crash if exactly three conditions were present.
• Moved the sam files containing all unmapped reads into a seperate directory. This was done to prevent a bug if the sample names end with '_unmapped'.

Changed (3 changes)

• Renamed category analyses in analysis.
• Renamed deseq2 module to dge-analysis.
• Renamed groups file in samples file.

- Python
Published by pblumenkamp over 5 years ago