Merge branch 'cw-5106' into 'dev'

Template v5.3.3 [CW-5106] See merge request epi2melabs/workflows/wf-somatic-variation!157
epi2me-labs · Dec 13, 2024 · f53d3da · f53d3da
2 parents 81de957 + 80c0987
commit f53d3da
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
           - epi2melabs==0.0.57
       - id: build_models
         name: build_models
-        entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py
+        entry: datamodel-codegen --strict-nullable --base-class workflow_glue.results_schema_helpers.BaseModel --use-subclass-enum --use-schema-description --disable-timestamp --input results_schema.yml --input-file-type openapi --output bin/workflow_glue/results_schema.py
         language: python
         files: 'results_schema.yml'
         pass_filenames: false

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.4.1]
+### Changed
+- Reconcile workflow with wf-template v5.3.3
+
 ## [v1.4.0]
 ### Added
 - BED files for the VNTR regions in hg19/hg38 from [Severus](https://github.com/KolmogorovLab/Severus/tree/main/vntrs).

diff --git a/bin/workflow_glue/__init__.py b/bin/workflow_glue/__init__.py
diff --git a/bin/workflow_glue/annotate_mutations.py b/bin/workflow_glue/annotate_mutations.py
diff --git a/bin/workflow_glue/check_bam_headers_in_dir.py b/bin/workflow_glue/check_bam_headers_in_dir.py
diff --git a/bin/workflow_glue/check_mapped_reads.py b/bin/workflow_glue/check_mapped_reads.py
diff --git a/bin/workflow_glue/check_sample_sheet.py b/bin/workflow_glue/check_sample_sheet.py
diff --git a/bin/workflow_glue/check_sq_ref.py b/bin/workflow_glue/check_sq_ref.py
diff --git a/bin/workflow_glue/check_valid_modbam.py b/bin/workflow_glue/check_valid_modbam.py
diff --git a/bin/workflow_glue/check_xam_index.py b/bin/workflow_glue/check_xam_index.py