docs: enhance documentation and workflow descriptions#240
Merged
visze merged 7 commits intokircherlab:developmentfrom Feb 4, 2026
Merged
docs: enhance documentation and workflow descriptions#240visze merged 7 commits intokircherlab:developmentfrom
visze merged 7 commits intokircherlab:developmentfrom
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visze
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Jan 27, 2026
visze
commented
- Updated the overview of the ASSIGNMENT and EXPERIMENT utilities in the documentation to clarify features and compatibility with BCalm.
- Added a new README.md file in the further documentation section, providing a tutorial overview and instructions for running notebooks locally and on Google Colab.
- Introduced a new adapter trimming section in the documentation, detailing the requirements and configuration for adapter trimming in both workflows.
- Created a tutorial section with Jupyter notebooks to assist users in understanding the workflow.
- Updated the plasmid example to fix design file headers and ensure compatibility with the pipeline.
- Enhanced the FAQ section to address design file requirements and clarify the need for overlapping paired-end reads.
- Updated the changelog inclusion method in the history documentation.
- Removed the outdated TODO list from the documentation.
- Updated diagrams for the assignment and experiment workflows to include optional adapter trimming.
- Made various adjustments to the configuration file documentation to improve clarity and usability.
- Updated the overview of the ASSIGNMENT and EXPERIMENT utilities in the documentation to clarify features and compatibility with BCalm. - Added a new README.md file in the further documentation section, providing a tutorial overview and instructions for running notebooks locally and on Google Colab. - Introduced a new adapter trimming section in the documentation, detailing the requirements and configuration for adapter trimming in both workflows. - Created a tutorial section with Jupyter notebooks to assist users in understanding the workflow. - Updated the plasmid example to fix design file headers and ensure compatibility with the pipeline. - Enhanced the FAQ section to address design file requirements and clarify the need for overlapping paired-end reads. - Updated the changelog inclusion method in the history documentation. - Removed the outdated TODO list from the documentation. - Updated diagrams for the assignment and experiment workflows to include optional adapter trimming. - Made various adjustments to the configuration file documentation to improve clarity and usability.
…for improved performance
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