fixing tests

Clinical-Genomics · Oct 5, 2023 · 0f1e54f · 0f1e54f
1 parent 2064b4f
commit 0f1e54f
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Showing 7 changed files with 19 additions and 7 deletions.
diff --git a/643594-miptest_metrics_deliverables.yaml b/643594-miptest_metrics_deliverables.yaml
@@ -0,0 +1,3 @@
+---
+metrics: []
+
diff --git a/definitions/rd_dna_panel_parameters.yaml b/definitions/rd_dna_panel_parameters.yaml
@@ -1183,7 +1183,7 @@ qccollect_eval_metric_file:
   associated_recipe:
     - qccollect_ar
   data_type: SCALAR
-  default: qc_eval_metric_-v1.3-.yaml
+  default: qc_eval_metric_-v1.4-.yaml
   exists_check: file
   is_reference: 1
   reference: reference_dir

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -2309,7 +2309,7 @@ qccollect_eval_metric_file:
   associated_recipe:
     - qccollect_ar
   data_type: SCALAR
-  default: qc_eval_metric_-v1.3-.yaml
+  default: qc_eval_metric_-v1.4-.yaml
   exists_check: file
   is_reference: 1
   reference: reference_dir

diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -1095,7 +1095,7 @@ qccollect_eval_metric_file:
   associated_recipe:
     - qccollect_ar
   data_type: SCALAR
-  default: qc_eval_metric_-v1.3-.yaml
+  default: qc_eval_metric_-v1.4-.yaml
   exists_check: file
   is_reference: 1
   reference: reference_dir

diff --git a/t/data/references/qc_eval_metric_-v1.3-.yaml → t/data/references/qc_eval_metric_-v1.4-.yaml b/t/data/references/qc_eval_metric_-v1.3-.yaml → t/data/references/qc_eval_metric_-v1.4-.yaml
@@ -28,6 +28,8 @@ wgs:
   collectmultiplemetrics:
     PCT_PF_READS_ALIGNED:
       lt: 0.95
+    PCT_PF_READS_IMPROPER_PAIRS:
+      gt: 0.05
     PCT_ADAPTER:
       gt: 0.0005
   markduplicates:

diff --git a/t/define_evaluate_metric.t b/t/define_evaluate_metric.t
@@ -47,8 +47,9 @@ diag(   q{Test define_evaluate_metric from Qccollect.pm}
       . $SPACE
       . $EXECUTABLE_NAME );
 
-Readonly my $PCT_ADAPTER          => 0.0005;
-Readonly my $PCT_PF_READS_ALIGNED => 0.95;
+Readonly my $PCT_ADAPTER                 => 0.0005;
+Readonly my $PCT_PF_READS_ALIGNED        => 0.95;
+Readonly my $PCT_PF_READS_IMPROPER_PAIRS => 0.05;
 
 my $log = test_log( { no_screen => 1, } );
 
@@ -59,7 +60,7 @@ my %sample_info = test_mip_hashes(
 );
 
 ## Given a file with evaluation metrics
-my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.3-.yaml} );
+my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.4-.yaml} );
 
 ## When defining the evaluation metrics based on the analysis
 my %evaluate_metric = define_evaluate_metric(
@@ -83,6 +84,9 @@ my %expected = (
             PCT_PF_READS_ALIGNED => {
                 lt => $PCT_PF_READS_ALIGNED,
             },
+            PCT_PF_READS_IMPROPER_PAIRS => {
+                gt => $PCT_PF_READS_IMPROPER_PAIRS,
+            },
         },
     },
     ADM1059A2 => {
@@ -98,6 +102,9 @@ my %expected = (
             PCT_PF_READS_ALIGNED => {
                 lt => $PCT_PF_READS_ALIGNED,
             },
+            PCT_PF_READS_IMPROPER_PAIRS => {
+                gt => $PCT_PF_READS_IMPROPER_PAIRS,
+            },
         },
     },
     ADM1059A3 => {

diff --git a/t/evaluate_analysis.t b/t/evaluate_analysis.t
@@ -69,7 +69,7 @@ my %sample_info = test_mip_hashes(
     }
 );
 
-my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.3-.yaml} );
+my $eval_metric_file = catfile( dirname($Bin), qw{ t data references qc_eval_metric_-v1.4-.yaml} );
 
 ## Then set the relevant evaluation metrics for the analysis
 my $is_ok = evaluate_analysis(