wip

bihealth · Jan 22, 2024 · fe1aa02 · fe1aa02
1 parent 71d1f4b
commit fe1aa02
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Showing 2 changed files with 2 additions and 12 deletions.
diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py
@@ -1204,9 +1204,6 @@ def _get_params_run(self, wildcards):
 
         return {
             "path_targets_bed": path_targets_bed,
-            "max_coverage": self.config["target_coverage_report"]["max_coverage"],
-            "min_cov_warning": self.config["target_coverage_report"]["min_cov_warning"],
-            "min_cov_ok": self.config["target_coverage_report"]["min_cov_ok"],
             "detailed_reporting": self.config["target_coverage_report"]["detailed_reporting"],
         }
 

diff --git a/snappy_pipeline/workflows/variant_export_external/__init__.py b/snappy_pipeline/workflows/variant_export_external/__init__.py
@@ -94,7 +94,7 @@
     ResourceUsage,
     WritePedigreeSampleNameStepPart,
 )
-from snappy_pipeline.workflows.ngs_mapping import TargetCoverageReportStepPart
+from snappy_pipeline.workflows.ngs_mapping import AlfredQcStepPart
 
 #: Default configuration for the somatic_variant_calling step
 DEFAULT_CONFIG = r"""
@@ -119,14 +119,10 @@
       # region coverage or selecting targeted exons. Only used if 'bam_available_flag' is True.
       # It will not generated detailed reporting.
       path_targets_bed: OPTIONAL # OPTIONAL
-      # Maximal/minimal/warning coverage
-      max_coverage: 200
-      min_cov_warning: 20  # >= 20x for WARNING
-      min_cov_ok: 50  # >= 50x for OK
 """
 
 
-class BamReportsExternalStepPart(TargetCoverageReportStepPart):
+class BamReportsExternalStepPart(AlfredQcStepPart):
     """Build target coverage report and QC report for external BAM files"""
 
     #: Step name
@@ -214,9 +210,6 @@ def _get_params_run(self, wildcards):
             "bam": sorted(list(self._collect_bam_files(wildcards))),
             "bam_count": len(sorted(list(self._collect_bam_files(wildcards)))),
             "path_targets_bed": self.config["target_coverage_report"]["path_targets_bed"],
-            "max_coverage": self.config["target_coverage_report"]["max_coverage"],
-            "min_cov_warning": self.config["target_coverage_report"]["min_cov_warning"],
-            "min_cov_ok": self.config["target_coverage_report"]["min_cov_ok"],
             "detailed_reporting": False,
         }