Merge e1b66da into d12e13a

Clinical-Genomics · Oct 9, 2023 · 4ae790b · 4ae790b
2 parents d12e13a + e1b66da
commit 4ae790b
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Showing 12 changed files with 21 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## Develop
+## [12.0.1]
 
 - Adds loqudb and gnomad frequencies to vcf2cytosure filtering
 - Store PCT_PF_READS_IMPROPER_PAIRS in qc file

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/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{12.0.0};
+Readonly our $MIP_VERSION => q{12.0.1};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

diff --git a/lib/MIP/Recipes/Install/Mip_scripts.pm b/lib/MIP/Recipes/Install/Mip_scripts.pm
@@ -88,7 +88,7 @@ sub install_mip_scripts {
               mip_rd_dna_vcf_rerun_config.yaml
               mip_rd_rna_config.yaml
               program_test_cmds.yaml
-              qc_eval_metric_-v1.3-.yaml
+              qc_eval_metric_-v1.4-.yaml
               qc_regexp_-v1.26-.yaml
               rank_model_-v1.34-.ini
               svrank_model_-v1.9-.ini

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(

diff --git a/t/mip_qccollect.test b/t/mip_qccollect.test
@@ -32,7 +32,7 @@ our $USAGE = build_usage( {} );
 my $VERBOSE = 1;
 ## Set paths
 my $cluster_constant_path = catdir( dirname($Bin), qw{ t data} );
-my $eval_metric_file      = catfile( dirname($Bin), qw{ templates qc_eval_metric_-v1.3-.yaml } );
+my $eval_metric_file      = catfile( dirname($Bin), qw{ templates qc_eval_metric_-v1.4-.yaml } );
 my $mip_path              = catfile( dirname($Bin), q{mip} );
 my $log_file_path         = catfile( cwd(),         q{qc_metrics_qccollect.log} );
 my $test_reference_path   = catdir( $cluster_constant_path, q{references} );

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v12.0.0
+    uri: docker.io/clinicalgenomics/mip:v12.0.1
   multiqc:
     executable:
       multiqc:

diff --git a/templates/qc_eval_metric_-v1.3-.yaml → templates/qc_eval_metric_-v1.4-.yaml b/templates/qc_eval_metric_-v1.3-.yaml → templates/qc_eval_metric_-v1.4-.yaml