samurai - v1.2.3.1 - "Nitta Yoshisada" hotfix

v1.2.3.1- [2025-07-22]

This release is a hotfix to ensure that ichorCNA panel of normals (PoN) built during the analysis (as opposed to using a pre-made one) will actually be used (before that the would get copied, but not included in the ichorCNA commands). Shout out to @LMannarino for finding the issue.

Bug Fixes

• Honor the PoN used, either as CLI argument or built during analysis(830f9e56597a4f351915440a838a051f454dd00c, @lbeltrame)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.2.3...v1.2.3.1

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Published by lbeltrame 11 months ago

samurai - v1.2.3 - "Nitta Yoshisada"

v1.2.3 - "Nitta Yoshisada" - [2025-07-21]

This release fixes a critical bug in the logR correction for GISTIC in ichorCNA, which caused wrong logR values to be generated. In addition, there are other fixes in ichorCNA (in particular now PoNs in data without chromosome X can be generated) and a small new feature (absolute integer CN in ASCAT.sc).

Nitta Yoshisada (新田義貞, 1301-1338) was a samurai lord during the Nanboku-cho period in Japan, also briefly involved in the wars following the so-called "Kenmu Restoration".

New Features

• Add integer absolute copy numbers to ASCAT.sc (#38, @SaraPotente)

Bug Fixes

• Fix GISTIC logR correction in ichorCNA (@lbeltrame, 002273536314d96f8446ee0e9cd84836af7ccf45)
• Make sure the ichorCNA PoN generation works even in absence of data on chrX (@lbeltrame, 5e292cef413676448f503f97660c395ee9ba0d99)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.2.2...v1.2.3

- Nextflow
Published by lbeltrame 11 months ago

samurai - v1.2.2 - "Shibata Katsuie"

v1.2.2 - "Shibata Katsuie" - [2025-07-10]

This release fixes a bug in the workflow caused by the new genomic plotting feature in the ichorCNA workflow.

Shibata Katsuie (柴田勝家; 1522-1583), also known with the name of Gonroku (権六) was a retainer of the Oda clan, serving under Oda Nobuhide and Oda Nobunaga during the "Warring States" period in Japan.

Bug Fixes

• Fix undefined output variable (9418166871a6504ea25470af5e8ef2393f216664, @SaraPotente)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.2.1...v1.2.2

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Published by lbeltrame 11 months ago

samurai - v1.2.1 - "Maeda Toshiie"

v1.2.1 - "Maeda Toshiie" - [2025-07-04]

This release fixes a bug in the new ichorCNA plotting introduced in version 1.2.0: plotting would not work due to a missing dependency in the container. A new container image has been made to correct this problem.

Maeda Toshiie (前田利家; 1538-1599), also known as "Yari no Mataza" (槍の又左) was a leading general under Oda Nobunaga during the "Warring States" period in Japan.

Bug Fixes

• Add missing svglite dependency to the container (@lbeltrame, 3a0f0760617bc1749614305b2883c4c19c114d00)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.2.0...v1.2.1

- Nextflow
Published by lbeltrame 11 months ago

samurai - v1.2.0

v1.2.0 - "Ohori Tsuruhime" - [2025-06-30]

This release adds support for ichorCNA in the solid biopsy workflow (see PR #42 for caveats) and new ploidy-aware plots for ichorCNA (off by default), which can be enabled by setting the option --ichorcna_ploidy_aware_plot.

This release is named after Ohori Tsuruhime (大祝鶴姫; 1526–1543), an "onna-musha" (female warrior) who lived and fought during the "Warring States" period in Japan. A suit of armor allegedly belonging to Tsuruhime is kept in the treasure hall of Oyamazumi Shrine, on the island of Omishima.

New features

• New plots for ichorCNA output (PR #44, @SaraPotente)
• Allow ichorCNA also in the solid biopsy workflow (PR #42, @lbeltrame)

Internal changes

• Move ichorCNA to a separate subworkflow

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.1.0...v1.2.0

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Published by lbeltrame 11 months ago

samurai - v1.1.0 - "Takeda Shingen"

v1.1.0 - "Takeda Shingen" - [2025-04-29]

This release introduces support for homologous recombination deficiency (HRD) detection using HRDCNA on top of the existing bug fixes from the 1.0.x. releases.

This release is named after Takeda Shingen (1521-1573), a warlord who ruled the province of Kai during the "Warring States" (Sengoku jidai) period.

New features

• HRDCNA integration by @SaraPotente in https://github.com/DIncalciLab/samurai/pull/35

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.7...v1.1.0

- Nextflow
Published by lbeltrame about 1 year ago

samurai - v.1.0.7

1.0.7 - Bug fix release

This release fixes a bug with ASCAT.sc summary tables being incorrectly saved if refitting was enabled (default). Thanks to @llanc-h for pointing out the problem.

Bug fixes

• Don't assume ASCAT.sc summary results are the same between refitted and non-refitted analyses (cb46c8ae8b31a5a56999795d9b7b8793caa43f9b)

- Nextflow
Published by lbeltrame about 1 year ago

samurai - v1.0.6

1.0.6 - Bug fix release

This release fixes a few bugs, some reported internally, some reported by users.

Bug fixes

• Fix genomic plot concatenations when running under Docker (#32)
• Allow running WisecondorX with size selection (8824631a699a33fa66fbe9c6b0021e021a64272f)

Internal changes

• Don't try to be too smart with HMMcopy's ReadCounter (1bbae5755acda8574b508ab93481fb5d0268cfc5)

- Nextflow
Published by lbeltrame over 1 year ago

samurai - v1.0.5

1.05 - Bug fix release

This release includes new documentation and a test profile to quickly evaluate SAMURAI using artificial data.

Documentation

• Add usage docs (PR #31, @SaraPotente) (#14)

Internal changes

• Rename test_ascat profile to test
• Fix some nf-core module linting

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.4...v1.0.5

- Nextflow
Published by lbeltrame over 1 year ago

samurai - v1.0.4 - Bug fix release

This is a bug fix release, addressing some bugs found during internal usage, and from initial feedback from external users.

What's Changed

Bug fixes

• Fix generating WisecondorX plots (@lbeltrame) (#28)

Internal changes

• Initial work towards implementation of a test profile (@SaraPotente) (#6)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.3...v1.0.4

- Nextflow
Published by lbeltrame over 1 year ago

samurai - 1.0.3 - Bug fix release

This is a bug fix release, addressing some bugs found during internal usage, and from initial feedback from external users.

What's Changed

Bug fixes

• Fix ichorCNA PoN generation (issue #20) - PR https://github.com/DIncalciLab/samurai/pull/22
• Fix iGenomes not being automatically downloaded (issue #19)

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.2...v1.0.3

- Nextflow
Published by lbeltrame over 1 year ago

samurai - 1.0.2 - Bug fix release

This is a bug fix release, solving an issue that caused the CIN signature workflow to fail.

Bug Fixes

• Fix CIN signature output file detection.

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.1...v1.0.2

- Nextflow
Published by lbeltrame over 1 year ago

samurai - 1.0.1 - Bug fix release

This is is a minor release which fixes a subtle but important bug found in the upstream gistic-cli project.

Bug Fixes

• Bump container version for gistic-cli to fix an off-by-one error in upstream gistic-cli.

Full Changelog: https://github.com/DIncalciLab/samurai/compare/v1.0.0...v1.0.1

- Nextflow
Published by lbeltrame over 1 year ago

samurai - 1.0.0 - Initial SAMURAI release

Initial release.

- Nextflow
Published by lbeltrame almost 2 years ago