Merge pull request #125 from d3b-center/release-0.14.0-🏷

🏷 Release 0.14.0

.github/ISSUE_TEMPLATE/submission_pkg_bug_report.yml

@@ -24,6 +24,7 @@ body:
       label: Version ID
       description: Select the version number relating to this bug
       options: # new_versions_here
+        - "0.14.0"
         - "0.13.0"
         - "0.12.0"
         - "0.11.1"

CHANGELOG.md

@@ -1,5 +1,28 @@
 # D3B CDS Manifest Prep Change History
 
+## Release 0.14.0
+
+### Updates to diagnoses
+
+This release includes a few updates to diagnoses:
+
+1. remove diagnoses from the histologies file that were manually assigned, that are attached to normal samples.
+2. Only include normal samples in the diagnosis-sample mapping table.
+3. test that only and all tumor samples are in the diagnosis-sample mapping table.
+4. if a participant's only samples in CDS are normal, and all of those samples only come from events that have only normal samples, extract the diagnoses from other events for the participant. Set the diagnosis ID to be based of the C-ID instead of the 7316 ID.
+
+### Summary
+
+- Emojis: 🐛 x2, ✅ x1
+- Categories: Additions x1, Fixes x2
+
+### New features and changes
+
+- [#124](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/124) - 🐛 Fix histologies file - [01269fdf](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/01269fdffb570810e6df5c310713a70b7e6e01b9) by [chris-s-friedman](https://github.com/chris-s-friedman)
+- [#123](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/123) - ✅ add test for diagnosis_sample map file - [38d8ddaa](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/38d8ddaa1584c951f314e78d34fe4c2dbf46e409) by [chris-s-friedman](https://github.com/chris-s-friedman)
+- [#122](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/122) - 🐛 missing diagnoses and remove normal samples from bs_dx - [ce3e2a9d](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/ce3e2a9deb6d8a517be556a0ea252ecf7d58f002) by [chris-s-friedman](https://github.com/chris-s-friedman)
+
+
 ## Release 0.13.0
 
 ### Set diagnosis as an attribute of event, not aliquot
@@ -353,4 +376,4 @@ Updated logic for picking diagnosis from pathology_diagnosis, broad_histology, a
 - [#4](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/4) - ✨ Add tools to generate manifests - [82049711](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/820497117ae34a6b01e69d93b44814508a99d371) by [chris-s-friedman](https://github.com/chris-s-friedman)
 - [#3](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/3) - ✨ Begin working on single entrypoint script - [ad18a5f0](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/ad18a5f0459886ad9b21f2dd858c7b189f6b2a69) by [chris-s-friedman](https://github.com/chris-s-friedman)
 - [#2](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/2) -  move qc script into its own step in pipeline - [c952f080](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/c952f08037f59f15c1178d46179638995bf842d9) by [chris-s-friedman](https://github.com/chris-s-friedman)
-- [#1](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/1) - 🚧 move files from kf_support and add extra cleanup - [de9dc1c6](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/de9dc1c63cdef88ef973fef42e3553bcd6eb1ec8) by [chris-s-friedman](https://github.com/chris-s-friedman)
+- [#1](https://github.com/d3b-center/d3b-cds-manifest-prep/pull/1) - 🚧 move files from kf_support and add extra cleanup - [de9dc1c6](https://github.com/d3b-center/d3b-cds-manifest-prep/commit/de9dc1c63cdef88ef973fef42e3553bcd6eb1ec8) by [chris-s-friedman](https://github.com/chris-s-friedman)

README.md

@@ -17,6 +17,7 @@ pip install git+https://github.com/d3b-center/d3b-cds-manifest-prep.git
 ## Data
 
 <!---line below is generated by prerelease script insert_version_url_here --->
+The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.14.0).
 The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.13.0).
 The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.12.0).
 The most recently generated manifest can be found [here](https://github.com/d3b-center/d3b-cds-manifest-prep/releases/tag/0.11.1).