Changelog

[0.1] - 04/06/2024

Initial release of the CNVand pipeline.

Added

CNV detection using CNVkit with target and antitarget coverage calculations, reference panel generation, systematic bias correction, CNV segmentation, and CNV calling.
CNV visualization with scatter plot generation in PDF and PNG formats.
Annotation using AnnotSV with reference gene annotations.
Docker support for pipeline execution in an isolated environment.
Snakedeploy support for quick installation.
Automated HTML report generation with Snakemake.

[0.2] - 05/06/2024

Minor changes in documentation and GitHub actions

Changed

GitHub workflow description under .github/workflows/dockerize.yml to exclude annotation bundling.
Mamba environment.yml file to set up an environment with the name 'cnvand'.
Main README.md to adapt to the former changes and to link to other documentation inside the repository.

[0.3] - 05/06/2024

Minor changes and fixes in CNVkit parameter handling

Changed

Fix missing passthrough of extra parameters in workflow/rules/cnv.smk and add a model option for the rule cnvkit_segment
Add the parameter from above as a seperate entry in config/config.yaml
Default model for the segment rule is now cbs

[0.4] - 07/11/2024

Added experimental feature to merge VCF and CNR files before annotation

Added rule in workflow/rules/cnv.smk to perform the merge of VCF and CNR files
Added getter method for annotSV rule to handle execution paths
Added config file option flag to activate the feature