v1.3.0 - "Uesugi Kenshin"

v1.3.0 - "Uesugi Kenshin" (2025-11-25)

This release brings a few bug fixes and a large internal reorganization to make the pipeline more robust. There are also a few new features, like better alignment parameters in BWA for cfDNA, support for read groups in BAM, and initial work towards using upstream nf-core modules.

This release is named after Uesugi Kenshin (上杉謙信, 1530-1578), also known as 越後の龍 (the dragon of Echigo), a powerful warrior ruling over the province of Echigo during the Sengoku period of feudal Japan. Kenshin and Takeda Shingen were notoriously rivals, and they allegedly fought against each other in personal combat during the fourth battle of Kawanakajima (1561).

New Features

• Support read groups (#54), @lbeltrame)
• Use optimized parameters for BWA alignment when dealing with cfDNA (#36, @lbeltrame) - Thanks to @SPPearce for the insight!
• Rename broad and focal in GISTIC output to long and short respectively to reduce the confusion with broad and focal lesions as defined by GISTIC itself (c3d17b8, @lbeltrame)

Bug Fixes

• Make pipeline parameters conditional (#23, @lbeltrame)
• Clamp ploidy aware log2ratios to -0.5 as lower bound to prevent nonsense results (e.g., -7) (6c02573, @lbeltrame)

Internal changes

• Remove usage of params as much as possible (#21, @lbeltrame)
• Use the upstream nf-core WisecondorX module and workflow(PR #51, @lbeltrame)
• Switch liquid biopsy to the common ichorCNA workflow (PR #55, @lbeltrame)