From cc3dae6088d9dd844de636d5aecd198c425457f6 Mon Sep 17 00:00:00 2001
From: Sebastian Allard <sebastian.allard@scilifelab.se>
Date: Fri, 12 Jan 2024 14:56:03 +0100
Subject: [PATCH] Add qc for non microbial samples in microsalt (#2825)(patch)

---
 cg/meta/upload/microsalt/microsalt_upload_api.py             | 2 +-
 cg/meta/workflow/microsalt/quality_controller/models.py      | 4 +---
 .../microsalt/quality_controller/quality_controller.py       | 4 ++++
 cg/meta/workflow/microsalt/quality_controller/utils.py       | 5 +++++
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/cg/meta/upload/microsalt/microsalt_upload_api.py b/cg/meta/upload/microsalt/microsalt_upload_api.py
index b4f31a48ec..69fb30739e 100644
--- a/cg/meta/upload/microsalt/microsalt_upload_api.py
+++ b/cg/meta/upload/microsalt/microsalt_upload_api.py
@@ -17,7 +17,7 @@ def __init__(self, config: CGConfig):
         super().__init__(config=config, analysis_api=self.analysis_api)
 
     def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
-        """Uploads MIP-DNA analysis data and files."""
+        """Uploads MicroSALT analysis data and files."""
         analysis: Analysis = case.analyses[0]
         self.update_upload_started_at(analysis)
 
diff --git a/cg/meta/workflow/microsalt/quality_controller/models.py b/cg/meta/workflow/microsalt/quality_controller/models.py
index f9579579c0..17100b82e6 100644
--- a/cg/meta/workflow/microsalt/quality_controller/models.py
+++ b/cg/meta/workflow/microsalt/quality_controller/models.py
@@ -1,13 +1,11 @@
 from pydantic import BaseModel
 
-from cg.constants.constants import MicrosaltAppTags
-
 
 class SampleQualityResult(BaseModel):
     sample_id: str
     passes_qc: bool
     is_control: bool
-    application_tag: MicrosaltAppTags
+    application_tag: str
     passes_reads_qc: bool
     passes_mapping_qc: bool = True
     passes_duplication_qc: bool = True
diff --git a/cg/meta/workflow/microsalt/quality_controller/quality_controller.py b/cg/meta/workflow/microsalt/quality_controller/quality_controller.py
index 8a00abb1e7..6f9a830fab 100644
--- a/cg/meta/workflow/microsalt/quality_controller/quality_controller.py
+++ b/cg/meta/workflow/microsalt/quality_controller/quality_controller.py
@@ -15,6 +15,7 @@
     get_percent_reads_guaranteed,
     get_report_path,
     get_sample_target_reads,
+    has_non_microbial_apptag,
     is_sample_negative_control,
     has_valid_10x_coverage,
     has_valid_average_coverage,
@@ -83,6 +84,9 @@ def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> Samp
             and valid_10x_coverage
         )
 
+        if has_non_microbial_apptag(sample):
+            sample_passes_qc = True
+
         sample_quality = SampleQualityResult(
             sample_id=sample_id,
             passes_qc=sample_passes_qc,
diff --git a/cg/meta/workflow/microsalt/quality_controller/utils.py b/cg/meta/workflow/microsalt/quality_controller/utils.py
index f1b4bdb525..3b6883e7bf 100644
--- a/cg/meta/workflow/microsalt/quality_controller/utils.py
+++ b/cg/meta/workflow/microsalt/quality_controller/utils.py
@@ -65,6 +65,11 @@ def has_valid_10x_coverage(metrics: SampleMetrics) -> bool:
     return is_valid_10x_coverage(coverage_10x) if coverage_10x else False
 
 
+def has_non_microbial_apptag(sample: Sample) -> bool:
+    app_tag: str = get_application_tag(sample)
+    return app_tag not in list(MicrosaltAppTags)
+
+
 def get_negative_control_result(results: list[SampleQualityResult]) -> SampleQualityResult | None:
     for result in results:
         if result.is_control: