v1.4.0 - "Ashikaga Takauji" (2025-12-11)

This release moves from an in-house snapshot of ichorCNA to the upstream nf-core (which required some fixes in ichorCNA and the bioconda package as well). It also moves away from the fragile "PoN files are gathered from a directory" to a more robust "normals are defined in the samplesheet". Notice that this version introduces significant breaking changes from the previous ones, which will require changes in workflow parameters. Make sure to read the section "Breaking changes" carefully before upgrading.

This release is named after Ashikaga Takauji (足利尊氏; 1305-1358), the founder of the Ashikaga shogunate during the Japanese Middle Ages, whose rise to power marked the beginning of the Muromachi period (1336-1576; "Muromachi" was the area of Kyoto where the Ashikaga took residence).

Breaking changes

• A new mandatory column has been added in the samplesheet, status, which can be either normal or tumor (@lbeltrame, issue #13)
• Option --pon_path has been removed. Instead, add your normal samples to the samplesheet (same rules as case samples) with the normal status
• Due to a bug in ichorCNA with security implications, the syntax of all options regarding ichorCNA chromosome handling (but not the readcounter parameters) has changed:
  • Specify chromosomes with identifier only (without chr)
  • Valid values are individual chromosomes, separated by comma (e.g. 1 or 1,2), ranges using : (1:22) or a combination of the above (1:22, X). If you set ichorcna_genomestyle, the right prefix will be appended for you when running the analysis
  • ichorcna_plotylim now takes a min and max value separated by comma (e.g. -2,4)
  • All the ichorCNA options that require TRUE or FALSE now take a boolean true or false
  • Raw R in any ichorCNA option (e.g. c(1,2)) is no longer supported and will raise an error.

New features

• Support the latest version of ichorCNA (@lbeltrame and @SaraPotente, PR #57)
• Fix generating panel of normals without sufficient reads on chromosome X (GavinHaLab/ichorCNA#26; bioconda/bioconda-recipes#61045; nf-core/modules#9531)
• Update the ichorCNA modules to the latest upstream nf-core versions (@lbeltrame, PR #57)
• PoN support in the samplesheet (@lbeltrame, #13, PR #57)

Bug fixes

• Don't raise an error if in CIN quantification there is only one sample (#59, @lbeltrame)