Merge pull request #398 from ypriverol/dev

Migration from python in house scripts to quantms-utils

.github/workflows/ci.yml

@@ -48,6 +48,8 @@ jobs:
             exec_profile: singularity
           - test_profile: test_lfq
             exec_profile: conda
+          - test_profile: test_dda_id
+            exec_profile: conda
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4

CHANGELOG.md

@@ -8,19 +8,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#386](https://github.com/bigbio/quantms/pull/386) Make validation of ontology terms optional
+- [#398](https://github.com/bigbio/quantms/pull/398) Python scripts moved to quantms-utils package
+- [#389](https://github.com/bigbio/quantms/pull/389) Introduction to DIANN 1.9.1 to the pipeline, only available in Singularity.
+- [#397](https://github.com/bigbio/quantms/pull/397) More options included in SDRF validation.
 
 ### Fixed
 
 - [#400](https://github.com/bigbio/quantms/pull/400) The random file selection when using `random_preanalysis` with DIANN is now reproducible.
 
 ### `Changed`
 
+- [#391](https://github.com/bigbio/quantms/pull/391) Move mzML statistics to parquet files from csv
+- [#386](https://github.com/bigbio/quantms/pull/386) Make optional the validation of ontology terms in the input SDRF file.
+- [#374](https://github.com/bigbio/quantms/pull/374) Create the common msgf+ database in one step before the msgf+ runs on each ms run file.
+-
+
 ### `Fixed`
 
 - [#396](https://github.com/bigbio/quantms/pull/396) Added verification of tar archive unpacking to prevent silent failures.
 
 ### `Dependencies`
 
+- quantms-utils==0.0.7
+- diann==1.9.1
+
 ### `Parameters`
 
 - `validate_ontologies`: enable or disable validating ontologies in the input SDRF file.