feat(balsamic-qc): Remove (#128)(major)

Remove BalsamicQC --------- Co-authored-by: Sebastian Diaz <[email protected]>
Clinical-Genomics · Feb 11, 2025 · 75661d3 · 75661d3
1 parent fa8747c
commit 75661d3
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Showing 7 changed files with 1 addition and 139 deletions.
diff --git a/cg_hermes/cli/validate.py b/cg_hermes/cli/validate.py
@@ -6,7 +6,6 @@
 
 from cg_hermes.cli.common import get_deliverables
 from cg_hermes.config.balsamic import BALSAMIC_TAGS
-from cg_hermes.config.balsamic_qc import BALSAMIC_QC_TAGS
 from cg_hermes.config.balsamic_umi import BALSAMIC_UMI_TAGS
 from cg_hermes.config.fluffy import FLUFFY_COMMON_TAGS
 from cg_hermes.config.mip_dna import MIP_DNA_TAGS
@@ -70,8 +69,6 @@ def validate_tags_cmd(workflow: Workflow) -> None:
         tag_map = BALSAMIC_TAGS
     elif workflow == Workflow.BALSAMIC_UMI:
         tag_map = BALSAMIC_UMI_TAGS
-    elif workflow == Workflow.BALSAMIC_QC:
-        tag_map = BALSAMIC_QC_TAGS
     elif workflow == Workflow.FLUFFY:
         tag_map = FLUFFY_COMMON_TAGS
     elif workflow == Workflow.MUTANT:

diff --git a/cg_hermes/config/balsamic_qc.py b/cg_hermes/config/balsamic_qc.py
diff --git a/cg_hermes/constants/workflow.py b/cg_hermes/constants/workflow.py
@@ -4,7 +4,6 @@
 class Workflow(StrEnum):
     BALSAMIC: str = "balsamic"
     BALSAMIC_PON: str = "balsamic-pon"
-    BALSAMIC_QC: str = "balsamic-qc"
     BALSAMIC_UMI: str = "balsamic-umi"
     DEMULTIPLEX: str = "demultiplex"
     FASTQ: str = "fastq"

diff --git a/cg_hermes/deliverables.py b/cg_hermes/deliverables.py
@@ -11,11 +11,6 @@
     TUMOR_ONLY_PANEL_TAGS,
     TUMOR_ONLY_WGS_TAGS,
 )
-from cg_hermes.config.balsamic_qc import (
-    BALSAMIC_QC_TAGS,
-    QC_TUMOR_NORMAL_PANEL_TAGS,
-    QC_TUMOR_NORMAL_WGS_TAGS,
-)
 from cg_hermes.config.balsamic_umi import (
     BALSAMIC_UMI_TAGS,
     UMI_TUMOR_NORMAL_PANEL_TAGS,
@@ -184,12 +179,6 @@ def get_balsamic_analysis_configs(self) -> dict[FrozenSet[str], dict]:
                 tag_set = TUMOR_ONLY_PANEL_TAGS
             else:
                 tag_set = TUMOR_NORMAL_PANEL_TAGS
-        elif self.workflow == Workflow.BALSAMIC_QC:
-            BALSAMIC_COMMON_TAGS = BALSAMIC_QC_TAGS
-            if self.analysis_type == CancerAnalysisType.TUMOR_NORMAL_WGS:
-                tag_set = QC_TUMOR_NORMAL_WGS_TAGS
-            elif self.analysis_type == CancerAnalysisType.TUMOR_NORMAL_PANEL:
-                tag_set = QC_TUMOR_NORMAL_PANEL_TAGS
         elif self.workflow == Workflow.BALSAMIC_UMI:
             BALSAMIC_COMMON_TAGS = BALSAMIC_UMI_TAGS
             if self.analysis_type == CancerAnalysisType.TUMOR_PANEL:

diff --git a/tests/cli/test_convert_command.py b/tests/cli/test_convert_command.py
@@ -210,50 +210,6 @@ def test_convert_balsamic_umi_t_only_deliverables(
     assert result.exit_code == 0
 
 
-def test_convert_balsamic_qc_tn_panel_deliverables(
-    cli_runner: CliRunner, balsamic_tn_panel_deliverables: Path
-):
-    # GIVEN the path to a balsamic deliverables file with TN data
-    assert balsamic_tn_panel_deliverables.exists()
-
-    # WHEN converting the deliverables to CG format
-    result = cli_runner.invoke(
-        app,
-        [
-            str(balsamic_tn_panel_deliverables),
-            "--workflow",
-            "balsamic-qc",
-            "--analysis-type",
-            "tumor_normal_panel",
-        ],
-    )
-
-    # THEN assert that the program exits with success
-    assert result.exit_code == 0
-
-
-def test_convert_balsamic_qc_tn_wgs_deliverables(
-    cli_runner: CliRunner, balsamic_tn_wgs_deliverables: Path
-):
-    # GIVEN the path to a balsamic deliverables file
-    assert balsamic_tn_wgs_deliverables.exists()
-
-    # WHEN converting the deliverables to CG format
-    result = cli_runner.invoke(
-        app,
-        [
-            str(balsamic_tn_wgs_deliverables),
-            "--workflow",
-            "balsamic-qc",
-            "--analysis-type",
-            "tumor_normal_wgs",
-        ],
-    )
-
-    # THEN assert that the program exits with success
-    assert result.exit_code == 0
-
-
 @pytest.mark.parametrize(
     "workflow",
     Workflow.get_nf_workflows(),

diff --git a/tests/cli/test_validate_deliverables_cmd.py b/tests/cli/test_validate_deliverables_cmd.py
@@ -79,30 +79,7 @@ def test_validate_balsamic_umi_deliverables_file(
         ],
     )
 
-    # THEN assert it exits without problem
-    assert result.exit_code == 0
-
-
-def test_validate_balsamic_qc_deliverables_file(
-    cli_runner: CliRunner, balsamic_tn_panel_deliverables: Path
-):
-    # GIVEN a existing balsamic deliverables file and a CLI runner
-    assert balsamic_tn_panel_deliverables.exists()
-
-    # WHEN running the validate deliverables command
-    result = cli_runner.invoke(
-        app,
-        [
-            "deliverables",
-            str(balsamic_tn_panel_deliverables),
-            "--workflow",
-            "balsamic-qc",
-            "--analysis-type",
-            "tumor_normal_panel",
-        ],
-    )
-
-    # THEN assert it exits without problem
+    # THEN assert it exits without a problem
     assert result.exit_code == 0
 
 

diff --git a/tests/cli/test_validate_tags.py b/tests/cli/test_validate_tags.py
@@ -37,16 +37,6 @@ def test_cli_validate_balsamic_umi_tags(cli_runner: CliRunner):
     assert result.exit_code == 0
 
 
-def test_cli_validate_balsamic_qc_tags(cli_runner: CliRunner):
-    # GIVEN a CLI runner
-
-    # WHEN testing to validate the common tags from the CLI
-    result = cli_runner.invoke(app, ["tags", "balsamic-qc"])
-
-    # THEN assert that the validation was successful
-    assert result.exit_code == 0
-
-
 def test_cli_validate_fluffy_tags(cli_runner: CliRunner):
     # GIVEN a CLI runner