Merge branch 'main' into rm-balsamic-qc

Clinical-Genomics · Feb 11, 2025 · ded0499 · ded0499
2 parents f67517a + fa8747c
commit ded0499
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Showing 10 changed files with 3 additions and 48 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.1.2
+current_version = 5.1.4
 commit = True
 tag = True
 tag_name = {new_version}

diff --git a/cg_hermes/config/balsamic.py b/cg_hermes/config/balsamic.py
@@ -7,7 +7,6 @@
 RAW_TAGS = {
     # Config, QC and reports (PANEL & WGS)
     "config.json": ["balsamic-config"],
-    "report.html": ["balsamic-report"],
     "BALSAMIC_X.X.X_graph.pdf": ["balsamic-dag"],
     "multiqc_report.html": ["html", "multiqc-html"],
     "multiqc_data.json": ["json", "multiqc-json"],
@@ -253,11 +252,6 @@
         "is_mandatory": True,
         "used_by": ["audit", "cg"],
     },
-    frozenset(RAW_TAGS["report.html"]): {  # BALSAMIC report html
-        "tags": ["balsamic-report"],
-        "is_mandatory": True,
-        "used_by": ["audit"],
-    },
     frozenset(RAW_TAGS["BALSAMIC_X.X.X_graph.pdf"]): {  # DAG
         "tags": ["balsamic-dag"],
         "is_mandatory": True,

diff --git a/cg_hermes/constants/hermes.py b/cg_hermes/constants/hermes.py
@@ -1 +1 @@
-HERMES_VERSION = "5.1.2"
+HERMES_VERSION = "5.1.4"
diff --git a/cg_hermes/constants/tags.py b/cg_hermes/constants/tags.py
@@ -518,7 +518,6 @@ def description(self) -> str:
 class BalsamicTags(StrEnum):
     BALSAMIC_CONFIG: str = "balsamic-config"
     BALSAMIC_DAG: str = "balsamic-dag"
-    BALSAMIC_REPORT: str = "balsamic-report"
 
     @classmethod
     def name(cls) -> str:
@@ -529,7 +528,6 @@ def description(self) -> str:
         descriptions: dict[str, BalsamicTags] = {
             self.BALSAMIC_CONFIG: "Balsamic configs for analysis",
             self.BALSAMIC_DAG: "Balsamic run schema",
-            self.BALSAMIC_REPORT: "Report from analysis",
         }
         return descriptions.get(self, "Description not available")
 

diff --git a/docs/balsamic_map.md b/docs/balsamic_map.md
@@ -1,7 +1,6 @@
 | Balsamic tags                                                  | Mandatory   | HK tags                                   | Used by               |
 |----------------------------------------------------------------|-------------|-------------------------------------------|-----------------------|
 | balsamic-config                                                | True        | balsamic-config                           | audit, cg             |
-| balsamic-report                                                | True        | balsamic-report                           | audit                 |
 | balsamic-dag                                                   | True        | balsamic-dag                              | audit                 |
 | html, multiqc-html                                             | True        | multiqc-html                              | audit, deliver, scout |
 | json, multiqc-json                                             | True        | multiqc-json                              | audit                 |

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cg-hermes"
-version = "5.1.2"
+version = "5.1.4"
 description = "Convert information between pipelines and CG"
 authors = ["Måns Magnusson <[email protected]>"]
 

diff --git a/tests/fixtures/balsamic/TN_panel.hk b/tests/fixtures/balsamic/TN_panel.hk
@@ -1082,15 +1082,6 @@
             "id": "TN-panel",
             "format": "stats"
         },
-        {
-            "path": "TN-panel/analysis/delivery_report/TN-panel_report.html",
-            "step": "balsamic_delivery",
-            "format": "html",
-            "tag": [
-                "balsamic-report"
-            ],
-            "id": "TN-panel"
-        },
         {
             "path": "TN-panel/TN-panel.json",
             "step": "case_config",

diff --git a/tests/fixtures/balsamic/TN_wgs.hk b/tests/fixtures/balsamic/TN_wgs.hk
@@ -890,15 +890,6 @@
             "id": "tumorsample",
             "format": "tbi"
         },
-        {
-            "path": "TN-wgs/analysis/delivery_report/TN-wgs_report.html",
-            "step": "balsamic_delivery",
-            "format": "html",
-            "tag": [
-                "balsamic-report"
-            ],
-            "id": "TN-wgs"
-        },
         {
             "path": "TN-wgs/TN-wgs.json",
             "step": "case_config",

diff --git a/tests/fixtures/balsamic/T_panel.hk b/tests/fixtures/balsamic/T_panel.hk
@@ -872,15 +872,6 @@
             "id": "tumorsample",
             "format": "crai"
         },
-        {
-            "path": "T-panel/analysis/delivery_report/T-panel_report.html",
-            "step": "balsamic_delivery",
-            "format": "html",
-            "tag": [
-                "balsamic-report"
-            ],
-            "id": "T-panel"
-        },
         {
             "path": "T-panel/T-panel.json",
             "step": "case_config",

diff --git a/tests/fixtures/balsamic/T_wgs.hk b/tests/fixtures/balsamic/T_wgs.hk
@@ -605,15 +605,6 @@
             "id": "215172",
             "format": "tbi"
         },
-        {
-            "path": "T-wgs/analysis/delivery_report/T-wgs_report.html",
-            "step": "balsamic_delivery",
-            "format": "html",
-            "tag": [
-                "balsamic-report"
-            ],
-            "id": "T-wgs"
-        },
         {
             "path": "T-wgs/T-wgs.json",
             "step": "case_config",