From 0eea407bebcb044da5ffb1b4918ba1f189eede2d Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 17 Jan 2025 12:51:54 -0600 Subject: [PATCH] Ad 5.1 release notes page --- docs/releases.rst | 1 + docs/releases/5_1.rst | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 docs/releases/5_1.rst diff --git a/docs/releases.rst b/docs/releases.rst index 5da0f741..60af6cde 100644 --- a/docs/releases.rst +++ b/docs/releases.rst @@ -22,3 +22,4 @@ Release Notes releases/4_3 releases/4_4 releases/5_0 + releases/5_1 diff --git a/docs/releases/5_1.rst b/docs/releases/5_1.rst new file mode 100644 index 00000000..5df2b3d6 --- /dev/null +++ b/docs/releases/5_1.rst @@ -0,0 +1,36 @@ +Version 5.1 +=========== + +Version 5.1.0 +------------- + +This is a minor feature release. It adds the following features: + +- This update allows pVACvector to remove peptides in order to find a partial solution if a full solution cannot be found. + The number of peptides permitted to be removed can be controlled by the ``--allow-n-peptide-exclusion`` parameter. by + @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1168 +- This update adds functionalities to pVACvector to prevent the core neoantigen candidate from getting clipped. by + @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1174 +- When only elution algorithms are chosen and no binding affinity algorithms, + the pipelines will now output a warning message that no aggregated report + can be created. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1165 +- When creating the aggregated report, the Best Peptide for some variants + may not match the aggregate inclusion criteria and no detail information + would be available for this peptide when investigating the variant. This + update ensures that the Best Peptide is always included in the metrics file + and counted toward the Num Included Peptides count. by @susannasiebert in + https://github.com/griffithlab/pVACtools/pull/1177 +- The evaluation buttons in pVACview will now be colored green for Accept, red + for Reject, and orange for Review to visually differentiate the different + statuses. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173 + +It also fixes the following problem(s): + +- This release removes two parameters from pVACvector: ``--aggregate-inclusion-binding-threshold`` and ``--aggregate-inclusion-count-limit`` + which are not applicable to this pipeline. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1180 +- This release fixes various pVACview bugs. Specifically, it fixes a bug that + would result in pVACview crashing when a variant with a Num Included + Peptides of 0 was selected. It also fixes a bug where re-tiering the + candidates before selecting evaluations would result in evaluations being + associated with incorrect variants. Additionally, it fixes several + deprecation warnings and typos. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173